diff --git a/end-to-end-test/local/specs/hide-download-controls.spec.js b/end-to-end-test/local/specs/hide-download-controls.spec.js
index e52c8d202be..863cf141dd8 100644
--- a/end-to-end-test/local/specs/hide-download-controls.spec.js
+++ b/end-to-end-test/local/specs/hide-download-controls.spec.js
@@ -457,6 +457,7 @@ describe('hide download controls feature', function() {
                 'Clinical Data',
                 'CN Segments',
                 'Files & Links',
+                'Plots Beta!',
                 'Study Sponsors',
             ];
             before(() => {
diff --git a/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png
index ea5f53ad2e2..34bc92a4ab0 100644
Binary files a/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png
index 3ee3fc1fb73..aa0f2266b67 100644
Binary files a/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/can_filter_a_study_by_sample_treatments_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png
index 3091084a6e2..3af4d1257ba 100644
Binary files a/end-to-end-test/remote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/check_for_survival_plots_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png
index 6ed07b3d015..fc4e35d177b 100644
Binary files a/end-to-end-test/remote/screenshots/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png
index eef23e5dc8e..64369ad037d 100644
Binary files a/end-to-end-test/remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png
index 72df0b82088..386bcbdd429 100644
Binary files a/end-to-end-test/remote/screenshots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png
index 2557d30ac57..f77072c7dc7 100644
Binary files a/end-to-end-test/remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png
index 211d5c8159e..f33e645b2a5 100644
Binary files a/end-to-end-test/remote/screenshots/reference/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png
index e8e72a9139f..31b36e4d4c9 100644
Binary files a/end-to-end-test/remote/screenshots/reference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png
index abf42292500..cb24ad5ec2e 100644
Binary files a/end-to-end-test/remote/screenshots/reference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/study_view_laml_tcga_clinical_data_clicked_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png
index e7d8fa378a1..2b0cc1b210f 100644
Binary files a/end-to-end-test/remote/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/screenshots/reference/when_quickly_adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/when_quickly_adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png
index 4b991440a79..f967ffcd6db 100644
Binary files a/end-to-end-test/remote/screenshots/reference/when_quickly_adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png and b/end-to-end-test/remote/screenshots/reference/when_quickly_adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png differ
diff --git a/end-to-end-test/remote/specs/core/customTabs.spec.js b/end-to-end-test/remote/specs/core/customTabs.spec.js
index 216e334156f..9fc32ce2c44 100644
--- a/end-to-end-test/remote/specs/core/customTabs.spec.js
+++ b/end-to-end-test/remote/specs/core/customTabs.spec.js
@@ -106,6 +106,11 @@ function runTests(pageName, url, tabLocation) {
 
             $('.mainTabs').waitForDisplayed();
 
+            if (tabLocation === 'STUDY_PAGE') {
+                $('i.fa-chevron-right').waitForDisplayed();
+                $('i.fa-chevron-right').click();
+            }
+
             assert.equal(
                 $('=Patient Tab').isDisplayed(),
                 false,
@@ -143,6 +148,11 @@ function runTests(pageName, url, tabLocation) {
 
             $('.mainTabs').waitForDisplayed();
 
+            if (tabLocation === 'STUDY_PAGE') {
+                $('i.fa-chevron-right').waitForDisplayed();
+                $('i.fa-chevron-right').click();
+            }
+
             assert.equal(
                 $('=Hidden Tab').isDisplayed(),
                 false,
@@ -235,7 +245,8 @@ function runTests(pageName, url, tabLocation) {
                 };
             });
 
-            $('=Async Tab').click();
+            // offset to avoid overlapping elements
+            $('=Async Tab').click({ x: -10 });
 
             browser.pause(1000);
 
diff --git a/src/pages/groupComparison/ClinicalData.tsx b/src/pages/groupComparison/ClinicalData.tsx
index a5be5e5a68c..80f3da4443c 100644
--- a/src/pages/groupComparison/ClinicalData.tsx
+++ b/src/pages/groupComparison/ClinicalData.tsx
@@ -31,7 +31,7 @@ import {
     isStringData,
     IStringAxisData,
     makeBoxScatterPlotData,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+} from 'shared/components/plots/PlotsTabUtils';
 import ScrollBar from 'shared/components/Scrollbar/ScrollBar';
 import { IBoxScatterPlotData } from 'shared/components/plots/BoxScatterPlot';
 import { scatterPlotSize } from 'shared/components/plots/PlotUtils';
diff --git a/src/pages/groupComparison/ClinicalNumericalDataVisualisation.tsx b/src/pages/groupComparison/ClinicalNumericalDataVisualisation.tsx
index 41641c018a7..6098a1c75cd 100644
--- a/src/pages/groupComparison/ClinicalNumericalDataVisualisation.tsx
+++ b/src/pages/groupComparison/ClinicalNumericalDataVisualisation.tsx
@@ -2,7 +2,7 @@ import BoxScatterPlot, {
     IBoxScatterPlotProps,
     toBoxPlotData,
 } from 'shared/components/plots/BoxScatterPlot';
-import { IBoxScatterPlotPoint } from 'pages/resultsView/plots/PlotsTabUtils';
+import { IBoxScatterPlotPoint } from 'shared/components/plots/PlotsTabUtils';
 import React from 'react';
 import { computed, makeObservable } from 'mobx';
 import { SummaryStatisticsTable } from './SummaryStatisticsTable';
diff --git a/src/pages/groupComparison/MultipleCategoryBarPlot.tsx b/src/pages/groupComparison/MultipleCategoryBarPlot.tsx
index 39b30d85fd9..ec6fa6e8dc8 100644
--- a/src/pages/groupComparison/MultipleCategoryBarPlot.tsx
+++ b/src/pages/groupComparison/MultipleCategoryBarPlot.tsx
@@ -31,7 +31,7 @@ import * as ReactDOM from 'react-dom';
 import { Popover } from 'react-bootstrap';
 import classnames from 'classnames';
 import { toConditionalPrecisionWithMinimum } from 'shared/lib/FormatUtils';
-import { IStringAxisData } from 'pages/resultsView/plots/PlotsTabUtils';
+import { IStringAxisData } from 'shared/components/plots/PlotsTabUtils';
 import WindowStore from 'shared/components/window/WindowStore';
 
 export interface IMultipleCategoryBarPlotProps {
diff --git a/src/pages/resultsView/ResultsViewPage.tsx b/src/pages/resultsView/ResultsViewPage.tsx
index 5c0d6bc1efd..09423eeade7 100644
--- a/src/pages/resultsView/ResultsViewPage.tsx
+++ b/src/pages/resultsView/ResultsViewPage.tsx
@@ -22,7 +22,7 @@ import StructuralVariants from 'pages/resultsView/structuralVariant/StructuralVa
 import './styles.scss';
 import ResultsViewOncoprint from 'shared/components/oncoprint/ResultsViewOncoprint';
 import QuerySummary from './querySummary/QuerySummary';
-import PlotsTab from './plots/PlotsTab';
+import PlotsTab from 'shared/components/plots/PlotsTab';
 import { MSKTab, MSKTabs } from '../../shared/components/MSKTabs/MSKTabs';
 import { PageLayout } from '../../shared/components/PageLayout/PageLayout';
 import autobind from 'autobind-decorator';
@@ -254,8 +254,97 @@ export default class ResultsViewPage extends React.Component<
                             linkText={'Plots'}
                         >
                             <PlotsTab
-                                store={store}
+                                filteredSamplesByDetailedCancerType={
+                                    store.filteredSamplesByDetailedCancerType
+                                }
+                                mutations={store.mutations}
+                                studies={store.studies}
+                                molecularProfileIdSuffixToMolecularProfiles={
+                                    store.molecularProfileIdSuffixToMolecularProfiles
+                                }
+                                entrezGeneIdToGene={store.entrezGeneIdToGene}
+                                sampleKeyToSample={store.sampleKeyToSample}
+                                genes={store.genes}
+                                clinicalAttributes={store.clinicalAttributes}
+                                genesets={store.genesets}
+                                genericAssayEntitiesGroupByMolecularProfileId={
+                                    store.genericAssayEntitiesGroupByMolecularProfileId
+                                }
+                                studyIds={store.studyIds}
+                                molecularProfilesWithData={
+                                    store.molecularProfilesWithData
+                                }
+                                molecularProfilesInStudies={
+                                    store.molecularProfilesInStudies
+                                }
+                                annotatedCnaCache={store.annotatedCnaCache}
+                                annotatedMutationCache={
+                                    store.annotatedMutationCache
+                                }
+                                structuralVariantCache={
+                                    store.structuralVariantCache
+                                }
+                                studyToMutationMolecularProfile={
+                                    store.studyToMutationMolecularProfile
+                                }
+                                studyToMolecularProfileDiscreteCna={
+                                    store.studyToMolecularProfileDiscreteCna
+                                }
+                                clinicalDataCache={store.clinicalDataCache}
+                                patientKeyToFilteredSamples={
+                                    store.patientKeyToFilteredSamples
+                                }
+                                numericGeneMolecularDataCache={
+                                    store.numericGeneMolecularDataCache
+                                }
+                                coverageInformation={store.coverageInformation}
+                                genesetMolecularDataCache={
+                                    store.genesetMolecularDataCache
+                                }
+                                genericAssayMolecularDataCache={
+                                    store.genericAssayMolecularDataCache
+                                }
+                                studyToStructuralVariantMolecularProfile={
+                                    store.studyToStructuralVariantMolecularProfile
+                                }
+                                driverAnnotationSettings={
+                                    store.driverAnnotationSettings
+                                }
+                                studyIdToStudy={store.studyIdToStudy.result}
+                                structuralVariants={
+                                    store.structuralVariants.result
+                                }
+                                hugoGeneSymbols={store.hugoGeneSymbols}
+                                selectedGenericAssayEntitiesGroupByMolecularProfileId={
+                                    store.selectedGenericAssayEntitiesGroupByMolecularProfileId
+                                }
+                                molecularProfileIdToMolecularProfile={
+                                    store.molecularProfileIdToMolecularProfile
+                                }
                                 urlWrapper={this.urlWrapper}
+                                queryContainsOql={store.queryContainsOql}
+                                includeGermlineMutations={
+                                    store.includeGermlineMutations
+                                }
+                                mutationsReportByGene={
+                                    store.mutationsReportByGene
+                                }
+                                oqlFilteredMutationsReport={
+                                    store.oqlFilteredMutationsReport
+                                }
+                                oqlFilteredMolecularDataReport={
+                                    store.oqlFilteredMolecularDataReport
+                                }
+                                oqlFilteredStructuralVariantsReport={
+                                    store.oqlFilteredStructuralVariantsReport
+                                }
+                                samples={store.samples}
+                                filteredSamples={store.filteredSamples}
+                                patients={store.patients}
+                                filteredPatients={store.filteredPatients}
+                                hideUnprofiledSamples={
+                                    store.hideUnprofiledSamples
+                                }
                             />
                         </MSKTab>
                     );
diff --git a/src/pages/resultsView/cancerSummary/CancerSummaryContainer.tsx b/src/pages/resultsView/cancerSummary/CancerSummaryContainer.tsx
index e9356ea1b92..53ee5ed98bd 100644
--- a/src/pages/resultsView/cancerSummary/CancerSummaryContainer.tsx
+++ b/src/pages/resultsView/cancerSummary/CancerSummaryContainer.tsx
@@ -235,11 +235,46 @@ export default class CancerSummaryContainer extends React.Component<
                         <div className={'tabMessageContainer'}>
                             <OqlStatusBanner
                                 className="cancer-types-summary-oql-status-banner"
-                                store={this.props.store}
+                                queryContainsOql={
+                                    this.props.store.queryContainsOql
+                                }
                                 tabReflectsOql={true}
                             />
-                            <AlterationFilterWarning store={this.props.store} />
-                            <CaseFilterWarning store={this.props.store} />
+                            <AlterationFilterWarning
+                                driverAnnotationSettings={
+                                    this.props.store.driverAnnotationSettings
+                                }
+                                includeGermlineMutations={
+                                    this.props.store.includeGermlineMutations
+                                }
+                                mutationsReportByGene={
+                                    this.props.store.mutationsReportByGene
+                                }
+                                oqlFilteredMutationsReport={
+                                    this.props.store.oqlFilteredMutationsReport
+                                }
+                                oqlFilteredMolecularDataReport={
+                                    this.props.store
+                                        .oqlFilteredMolecularDataReport
+                                }
+                                oqlFilteredStructuralVariantsReport={
+                                    this.props.store
+                                        .oqlFilteredStructuralVariantsReport
+                                }
+                            />
+                            <CaseFilterWarning
+                                samples={this.props.store.samples}
+                                filteredSamples={
+                                    this.props.store.filteredSamples
+                                }
+                                patients={this.props.store.patients}
+                                filteredPatients={
+                                    this.props.store.filteredPatients
+                                }
+                                hideUnprofiledSamples={
+                                    this.props.store.hideUnprofiledSamples
+                                }
+                            />
                         </div>
                         <MSKTabs
                             onTabClick={this.handleTabClick}
diff --git a/src/pages/resultsView/cnSegments/CNSegments.tsx b/src/pages/resultsView/cnSegments/CNSegments.tsx
index 9bb7b8daba0..f939c6e456b 100644
--- a/src/pages/resultsView/cnSegments/CNSegments.tsx
+++ b/src/pages/resultsView/cnSegments/CNSegments.tsx
@@ -184,7 +184,15 @@ export default class CNSegments extends React.Component<
                     }
                 />
                 <div className={'tabMessageContainer'}>
-                    <CaseFilterWarning store={this.props.store} />
+                    <CaseFilterWarning
+                        samples={this.props.store.samples}
+                        filteredSamples={this.props.store.filteredSamples}
+                        patients={this.props.store.patients}
+                        filteredPatients={this.props.store.filteredPatients}
+                        hideUnprofiledSamples={
+                            this.props.store.hideUnprofiledSamples
+                        }
+                    />
                 </div>
                 <Nav
                     bsStyle="pills"
diff --git a/src/pages/resultsView/coExpression/CoExpressionPlot.tsx b/src/pages/resultsView/coExpression/CoExpressionPlot.tsx
index 3d7db79f4a7..edf0334857c 100644
--- a/src/pages/resultsView/coExpression/CoExpressionPlot.tsx
+++ b/src/pages/resultsView/coExpression/CoExpressionPlot.tsx
@@ -17,7 +17,7 @@ import {
 } from './CoExpressionPlotUtils';
 import _ from 'lodash';
 import { scatterPlotSize } from '../../../shared/components/plots/PlotUtils';
-import { IAxisLogScaleParams } from 'pages/resultsView/plots/PlotsTabUtils';
+import { IAxisLogScaleParams } from 'shared/components/plots/PlotsTabUtils';
 import autobind from 'autobind-decorator';
 import { GeneticEntity } from 'shared/model/GeneticEntity';
 import { getServerConfig } from 'config/config';
diff --git a/src/pages/resultsView/coExpression/CoExpressionPlotUtils.ts b/src/pages/resultsView/coExpression/CoExpressionPlotUtils.ts
index 7102a85c465..c72c545e62e 100644
--- a/src/pages/resultsView/coExpression/CoExpressionPlotUtils.ts
+++ b/src/pages/resultsView/coExpression/CoExpressionPlotUtils.ts
@@ -1,5 +1,5 @@
 import _ from 'lodash';
-import { IAxisLogScaleParams } from 'pages/resultsView/plots/PlotsTabUtils';
+import { IAxisLogScaleParams } from 'shared/components/plots/PlotsTabUtils';
 import { CoExpressionPlotData } from 'pages/resultsView/coExpression/CoExpressionPlot';
 import { MolecularProfile } from 'cbioportal-ts-api-client';
 import { GeneticEntity } from 'shared/model/GeneticEntity';
diff --git a/src/pages/resultsView/coExpression/CoExpressionTab.tsx b/src/pages/resultsView/coExpression/CoExpressionTab.tsx
index a88640b7f54..31facb6a223 100644
--- a/src/pages/resultsView/coExpression/CoExpressionTab.tsx
+++ b/src/pages/resultsView/coExpression/CoExpressionTab.tsx
@@ -652,14 +652,39 @@ export default class CoExpressionTab extends React.Component<
                 <div className={'tabMessageContainer'}>
                     <OqlStatusBanner
                         className="coexp-oql-status-banner"
-                        store={this.props.store}
+                        queryContainsOql={this.props.store.queryContainsOql}
                         tabReflectsOql={false}
                     />
                     <AlterationFilterWarning
-                        store={this.props.store}
+                        driverAnnotationSettings={
+                            this.props.store.driverAnnotationSettings
+                        }
+                        includeGermlineMutations={
+                            this.props.store.includeGermlineMutations
+                        }
+                        mutationsReportByGene={
+                            this.props.store.mutationsReportByGene
+                        }
+                        oqlFilteredMutationsReport={
+                            this.props.store.oqlFilteredMutationsReport
+                        }
+                        oqlFilteredMolecularDataReport={
+                            this.props.store.oqlFilteredMolecularDataReport
+                        }
+                        oqlFilteredStructuralVariantsReport={
+                            this.props.store.oqlFilteredStructuralVariantsReport
+                        }
                         isUnaffected={true}
                     />
-                    <CaseFilterWarning store={this.props.store} />
+                    <CaseFilterWarning
+                        samples={this.props.store.samples}
+                        filteredSamples={this.props.store.filteredSamples}
+                        patients={this.props.store.patients}
+                        filteredPatients={this.props.store.filteredPatients}
+                        hideUnprofiledSamples={
+                            this.props.store.hideUnprofiledSamples
+                        }
+                    />
                 </div>
 
                 {status === 'complete' && divContents}
diff --git a/src/pages/resultsView/coExpression/CoExpressionViz.tsx b/src/pages/resultsView/coExpression/CoExpressionViz.tsx
index 8b8daa1b144..c240e5ff6e5 100644
--- a/src/pages/resultsView/coExpression/CoExpressionViz.tsx
+++ b/src/pages/resultsView/coExpression/CoExpressionViz.tsx
@@ -18,7 +18,7 @@ import {
 } from 'mobx';
 import LoadingIndicator from 'shared/components/loadingIndicator/LoadingIndicator';
 import { SimpleGetterLazyMobXTableApplicationDataStore } from '../../../shared/lib/ILazyMobXTableApplicationDataStore';
-import { logScalePossibleForProfile } from '../plots/PlotsTabUtils';
+import { logScalePossibleForProfile } from 'shared/components/plots/PlotsTabUtils';
 import CoExpressionPlot, { ICoExpressionPlotProps } from './CoExpressionPlot';
 import { MobxPromise, remoteData } from 'cbioportal-frontend-commons';
 import { computePlotData, requestAllDataMessage } from './CoExpressionVizUtils';
diff --git a/src/pages/resultsView/comparison/ComparisonTab.tsx b/src/pages/resultsView/comparison/ComparisonTab.tsx
index 286fb7dbe63..95a412ed973 100644
--- a/src/pages/resultsView/comparison/ComparisonTab.tsx
+++ b/src/pages/resultsView/comparison/ComparisonTab.tsx
@@ -327,11 +327,38 @@ export default class ComparisonTab extends React.Component<
                 >
                     <OqlStatusBanner
                         className="comparison-oql-status-banner"
-                        store={this.props.store}
+                        queryContainsOql={this.props.store.queryContainsOql}
                         tabReflectsOql={true}
                     />
-                    <AlterationFilterWarning store={this.props.store} />
-                    <CaseFilterWarning store={this.props.store} />
+                    <AlterationFilterWarning
+                        driverAnnotationSettings={
+                            this.props.store.driverAnnotationSettings
+                        }
+                        includeGermlineMutations={
+                            this.props.store.includeGermlineMutations
+                        }
+                        mutationsReportByGene={
+                            this.props.store.mutationsReportByGene
+                        }
+                        oqlFilteredMutationsReport={
+                            this.props.store.oqlFilteredMutationsReport
+                        }
+                        oqlFilteredMolecularDataReport={
+                            this.props.store.oqlFilteredMolecularDataReport
+                        }
+                        oqlFilteredStructuralVariantsReport={
+                            this.props.store.oqlFilteredStructuralVariantsReport
+                        }
+                    />
+                    <CaseFilterWarning
+                        samples={this.props.store.samples}
+                        filteredSamples={this.props.store.filteredSamples}
+                        patients={this.props.store.patients}
+                        filteredPatients={this.props.store.filteredPatients}
+                        hideUnprofiledSamples={
+                            this.props.store.hideUnprofiledSamples
+                        }
+                    />
                 </div>
                 <div
                     style={{
diff --git a/src/pages/resultsView/download/DownloadTab.tsx b/src/pages/resultsView/download/DownloadTab.tsx
index 3df3ef1fa97..c2ce9ba5a18 100644
--- a/src/pages/resultsView/download/DownloadTab.tsx
+++ b/src/pages/resultsView/download/DownloadTab.tsx
@@ -675,11 +675,46 @@ export default class DownloadTab extends React.Component<
                         <div className={'tabMessageContainer'}>
                             <OqlStatusBanner
                                 className="download-oql-status-banner"
-                                store={this.props.store}
+                                queryContainsOql={
+                                    this.props.store.queryContainsOql
+                                }
                                 tabReflectsOql={true}
                             />
-                            <AlterationFilterWarning store={this.props.store} />
-                            <CaseFilterWarning store={this.props.store} />
+                            <AlterationFilterWarning
+                                driverAnnotationSettings={
+                                    this.props.store.driverAnnotationSettings
+                                }
+                                includeGermlineMutations={
+                                    this.props.store.includeGermlineMutations
+                                }
+                                mutationsReportByGene={
+                                    this.props.store.mutationsReportByGene
+                                }
+                                oqlFilteredMutationsReport={
+                                    this.props.store.oqlFilteredMutationsReport
+                                }
+                                oqlFilteredMolecularDataReport={
+                                    this.props.store
+                                        .oqlFilteredMolecularDataReport
+                                }
+                                oqlFilteredStructuralVariantsReport={
+                                    this.props.store
+                                        .oqlFilteredStructuralVariantsReport
+                                }
+                            />
+                            <CaseFilterWarning
+                                samples={this.props.store.samples}
+                                filteredSamples={
+                                    this.props.store.filteredSamples
+                                }
+                                patients={this.props.store.patients}
+                                filteredPatients={
+                                    this.props.store.filteredPatients
+                                }
+                                hideUnprofiledSamples={
+                                    this.props.store.hideUnprofiledSamples
+                                }
+                            />
                         </div>
                         <div>
                             <FeatureTitle
diff --git a/src/pages/resultsView/enrichments/ExpressionEnrichmentsBoxPlot.tsx b/src/pages/resultsView/enrichments/ExpressionEnrichmentsBoxPlot.tsx
index c5afa360b51..49feca72e59 100644
--- a/src/pages/resultsView/enrichments/ExpressionEnrichmentsBoxPlot.tsx
+++ b/src/pages/resultsView/enrichments/ExpressionEnrichmentsBoxPlot.tsx
@@ -17,7 +17,7 @@ import {
     INumberAxisData,
     makeBoxScatterPlotData,
     getBoxPlotDownloadData,
-} from '../plots/PlotsTabUtils';
+} from 'shared/components/plots/PlotsTabUtils';
 import BoxScatterPlot, {
     IBoxScatterPlotData,
 } from 'shared/components/plots/BoxScatterPlot';
diff --git a/src/pages/resultsView/enrichments/GenericAssayCategoricalEnrichmentsContainer.tsx b/src/pages/resultsView/enrichments/GenericAssayCategoricalEnrichmentsContainer.tsx
index e464a6c404f..9cade505c06 100644
--- a/src/pages/resultsView/enrichments/GenericAssayCategoricalEnrichmentsContainer.tsx
+++ b/src/pages/resultsView/enrichments/GenericAssayCategoricalEnrichmentsContainer.tsx
@@ -34,7 +34,7 @@ import {
     IAxisData,
     IAxisLogScaleParams,
     IStringAxisData,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+} from 'shared/components/plots/PlotsTabUtils';
 import CategoryPlot, {
     CategoryPlotType,
 } from 'pages/groupComparison/CategoryPlot';
diff --git a/src/pages/resultsView/expression/ExpressionWrapper.tsx b/src/pages/resultsView/expression/ExpressionWrapper.tsx
index 1d601acb780..cff38a06ef0 100644
--- a/src/pages/resultsView/expression/ExpressionWrapper.tsx
+++ b/src/pages/resultsView/expression/ExpressionWrapper.tsx
@@ -36,7 +36,7 @@ import {
     scatterPlotZIndexSortBy,
     IAxisLogScaleParams,
     basicAppearance,
-} from '../plots/PlotsTabUtils';
+} from 'shared/components/plots/PlotsTabUtils';
 import { ResultsViewPageStore } from '../ResultsViewPageStore';
 import OqlStatusBanner from '../../../shared/components/banners/OqlStatusBanner';
 import {
@@ -53,7 +53,7 @@ import {
     ColoringType,
     PlotType,
     SelectedColoringTypes,
-} from '../plots/PlotsTab';
+} from '../../../shared/components/plots/PlotsTab';
 import AlterationFilterWarning from '../../../shared/components/banners/AlterationFilterWarning';
 import CaseFilterWarning from '../../../shared/components/banners/CaseFilterWarning';
 import { getBoxWidth } from 'shared/lib/boxPlotUtils';
@@ -721,12 +721,39 @@ export default class ExpressionWrapper extends React.Component<
                 <div className={'tabMessageContainer'}>
                     <OqlStatusBanner
                         className="expression-oql-status-banner"
-                        store={this.props.store}
+                        queryContainsOql={this.props.store.queryContainsOql}
                         tabReflectsOql={false}
                         style={{ marginTop: -1, marginBottom: 12 }}
                     />
-                    <AlterationFilterWarning store={this.props.store} />
-                    <CaseFilterWarning store={this.props.store} />
+                    <AlterationFilterWarning
+                        driverAnnotationSettings={
+                            this.props.store.driverAnnotationSettings
+                        }
+                        includeGermlineMutations={
+                            this.props.store.includeGermlineMutations
+                        }
+                        mutationsReportByGene={
+                            this.props.store.mutationsReportByGene
+                        }
+                        oqlFilteredMutationsReport={
+                            this.props.store.oqlFilteredMutationsReport
+                        }
+                        oqlFilteredMolecularDataReport={
+                            this.props.store.oqlFilteredMolecularDataReport
+                        }
+                        oqlFilteredStructuralVariantsReport={
+                            this.props.store.oqlFilteredStructuralVariantsReport
+                        }
+                    />
+                    <CaseFilterWarning
+                        samples={this.props.store.samples}
+                        filteredSamples={this.props.store.filteredSamples}
+                        patients={this.props.store.patients}
+                        filteredPatients={this.props.store.filteredPatients}
+                        hideUnprofiledSamples={
+                            this.props.store.hideUnprofiledSamples
+                        }
+                    />
                 </div>
                 {this.studySelectorModalVisible && this.studySelectionModal}
                 <div style={{ marginBottom: 15 }}>
diff --git a/src/pages/resultsView/expression/expressionHelpers.tsx b/src/pages/resultsView/expression/expressionHelpers.tsx
index 55df304b5e0..880a5e00df3 100644
--- a/src/pages/resultsView/expression/expressionHelpers.tsx
+++ b/src/pages/resultsView/expression/expressionHelpers.tsx
@@ -14,7 +14,7 @@ import {
     mutationRenderPriority,
     tooltipCnaSection,
     tooltipMutationsSection,
-} from '../plots/PlotsTabUtils';
+} from 'shared/components/plots/PlotsTabUtils';
 import { getJitterForCase } from '../../../shared/components/plots/PlotUtils';
 import * as React from 'react';
 import { getSampleViewUrl, getStudySummaryUrl } from '../../../shared/api/urls';
diff --git a/src/pages/resultsView/mutation/Mutations.tsx b/src/pages/resultsView/mutation/Mutations.tsx
index 9dc344b8614..9c098d005ff 100644
--- a/src/pages/resultsView/mutation/Mutations.tsx
+++ b/src/pages/resultsView/mutation/Mutations.tsx
@@ -184,7 +184,7 @@ export default class Mutations extends React.Component<
                     <div className={'tabMessageContainer'}>
                         <OqlStatusBanner
                             className="mutations-oql-status-banner"
-                            store={this.props.store}
+                            queryContainsOql={this.props.store.queryContainsOql}
                             tabReflectsOql={
                                 this.props.store.mutationsTabFilteringSettings
                                     .useOql
@@ -195,7 +195,25 @@ export default class Mutations extends React.Component<
                             onToggle={this.onToggleOql}
                         />
                         <AlterationFilterWarning
-                            store={this.props.store}
+                            driverAnnotationSettings={
+                                this.props.store.driverAnnotationSettings
+                            }
+                            includeGermlineMutations={
+                                this.props.store.includeGermlineMutations
+                            }
+                            mutationsReportByGene={
+                                this.props.store.mutationsReportByGene
+                            }
+                            oqlFilteredMutationsReport={
+                                this.props.store.oqlFilteredMutationsReport
+                            }
+                            oqlFilteredMolecularDataReport={
+                                this.props.store.oqlFilteredMolecularDataReport
+                            }
+                            oqlFilteredStructuralVariantsReport={
+                                this.props.store
+                                    .oqlFilteredStructuralVariantsReport
+                            }
                             mutationsTabModeSettings={{
                                 excludeVUS: this.props.store
                                     .mutationsTabFilteringSettings.excludeVus,
@@ -208,7 +226,15 @@ export default class Mutations extends React.Component<
                                     .hugoGeneSymbol,
                             }}
                         />
-                        <CaseFilterWarning store={this.props.store} />
+                        <CaseFilterWarning
+                            samples={this.props.store.samples}
+                            filteredSamples={this.props.store.filteredSamples}
+                            patients={this.props.store.patients}
+                            filteredPatients={this.props.store.filteredPatients}
+                            hideUnprofiledSamples={
+                                this.props.store.hideUnprofiledSamples
+                            }
+                        />
                     </div>
                     <ResultsViewMutationMapper
                         {...convertToMutationMapperProps({
diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityTab.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityTab.tsx
index f4a229064f2..f2d756ddf28 100644
--- a/src/pages/resultsView/mutualExclusivity/MutualExclusivityTab.tsx
+++ b/src/pages/resultsView/mutualExclusivity/MutualExclusivityTab.tsx
@@ -119,7 +119,9 @@ export default class MutualExclusivityTab extends React.Component<
                             <div className={'tabMessageContainer'}>
                                 <OqlStatusBanner
                                     className="mutex-oql-status-banner"
-                                    store={this.props.store}
+                                    queryContainsOql={
+                                        this.props.store.queryContainsOql
+                                    }
                                     tabReflectsOql={true}
                                 />
                                 {this.filteredTrackOqls.length > 0 && (
@@ -131,9 +133,43 @@ export default class MutualExclusivityTab extends React.Component<
                                     </div>
                                 )}
                                 <AlterationFilterWarning
-                                    store={this.props.store}
+                                    driverAnnotationSettings={
+                                        this.props.store
+                                            .driverAnnotationSettings
+                                    }
+                                    includeGermlineMutations={
+                                        this.props.store
+                                            .includeGermlineMutations
+                                    }
+                                    mutationsReportByGene={
+                                        this.props.store.mutationsReportByGene
+                                    }
+                                    oqlFilteredMutationsReport={
+                                        this.props.store
+                                            .oqlFilteredMutationsReport
+                                    }
+                                    oqlFilteredMolecularDataReport={
+                                        this.props.store
+                                            .oqlFilteredMolecularDataReport
+                                    }
+                                    oqlFilteredStructuralVariantsReport={
+                                        this.props.store
+                                            .oqlFilteredStructuralVariantsReport
+                                    }
+                                />
+                                <CaseFilterWarning
+                                    samples={this.props.store.samples}
+                                    filteredSamples={
+                                        this.props.store.filteredSamples
+                                    }
+                                    patients={this.props.store.patients}
+                                    filteredPatients={
+                                        this.props.store.filteredPatients
+                                    }
+                                    hideUnprofiledSamples={
+                                        this.props.store.hideUnprofiledSamples
+                                    }
                                 />
-                                <CaseFilterWarning store={this.props.store} />
                             </div>
                         )}
 
@@ -178,9 +214,40 @@ export default class MutualExclusivityTab extends React.Component<
                         )}
                         {this.props.store && [
                             <AlterationFilterWarning
-                                store={this.props.store}
+                                driverAnnotationSettings={
+                                    this.props.store.driverAnnotationSettings
+                                }
+                                includeGermlineMutations={
+                                    this.props.store.includeGermlineMutations
+                                }
+                                mutationsReportByGene={
+                                    this.props.store.mutationsReportByGene
+                                }
+                                oqlFilteredMutationsReport={
+                                    this.props.store.oqlFilteredMutationsReport
+                                }
+                                oqlFilteredMolecularDataReport={
+                                    this.props.store
+                                        .oqlFilteredMolecularDataReport
+                                }
+                                oqlFilteredStructuralVariantsReport={
+                                    this.props.store
+                                        .oqlFilteredStructuralVariantsReport
+                                }
+                            />,
+                            <CaseFilterWarning
+                                samples={this.props.store.samples}
+                                filteredSamples={
+                                    this.props.store.filteredSamples
+                                }
+                                patients={this.props.store.patients}
+                                filteredPatients={
+                                    this.props.store.filteredPatients
+                                }
+                                hideUnprofiledSamples={
+                                    this.props.store.hideUnprofiledSamples
+                                }
                             />,
-                            <CaseFilterWarning store={this.props.store} />,
                         ]}
                     </div>
                 );
diff --git a/src/pages/resultsView/pathwayMapper/ResultsViewPathwayMapper.tsx b/src/pages/resultsView/pathwayMapper/ResultsViewPathwayMapper.tsx
index 8ef196a9790..cc52fe7c861 100644
--- a/src/pages/resultsView/pathwayMapper/ResultsViewPathwayMapper.tsx
+++ b/src/pages/resultsView/pathwayMapper/ResultsViewPathwayMapper.tsx
@@ -209,7 +209,9 @@ export default class ResultsViewPathwayMapper extends React.Component<
                         <React.Fragment>
                             <OqlStatusBanner
                                 className="coexp-oql-status-banner"
-                                store={this.props.store}
+                                queryContainsOql={
+                                    this.props.store.queryContainsOql
+                                }
                                 tabReflectsOql={true}
                             />
                             {/*
diff --git a/src/pages/studyView/StudyViewPage.tsx b/src/pages/studyView/StudyViewPage.tsx
index d2229ae227e..508fe36e461 100644
--- a/src/pages/studyView/StudyViewPage.tsx
+++ b/src/pages/studyView/StudyViewPage.tsx
@@ -78,6 +78,7 @@ import {
     prepareCustomTabConfigurations,
 } from 'shared/lib/customTabs/customTabHelpers';
 import { VirtualStudyModal } from 'pages/studyView/virtualStudy/VirtualStudyModal';
+import PlotsTab from 'shared/components/plots/PlotsTab';
 
 export interface IStudyViewPageProps {
     routing: any;
@@ -733,6 +734,142 @@ export default class StudyViewPage extends React.Component<
                                             />
                                         </div>
                                     </MSKTab>
+                                    <MSKTab
+                                        key={5}
+                                        id={StudyViewPageTabKeyEnum.PLOTS}
+                                        linkText={
+                                            <span>
+                                                {
+                                                    StudyViewPageTabDescriptions.PLOTS
+                                                }{' '}
+                                                <strong className={'beta-text'}>
+                                                    Beta!
+                                                </strong>
+                                            </span>
+                                        }
+                                    >
+                                        <PlotsTab
+                                            filteredSamplesByDetailedCancerType={
+                                                this.store
+                                                    .filteredSamplesByDetailedCancerType
+                                            }
+                                            mutations={this.store.mutations}
+                                            studies={
+                                                this.store
+                                                    .queriedPhysicalStudies
+                                            }
+                                            molecularProfileIdSuffixToMolecularProfiles={
+                                                this.store
+                                                    .molecularProfileIdSuffixToMolecularProfiles
+                                            }
+                                            entrezGeneIdToGene={
+                                                this.store.entrezGeneIdToGeneAll
+                                            }
+                                            sampleKeyToSample={
+                                                this.store.sampleSetByKey
+                                            }
+                                            genes={this.store.allGenes}
+                                            clinicalAttributes={
+                                                this.store.clinicalAttributes
+                                            }
+                                            genesets={this.store.genesets}
+                                            genericAssayEntitiesGroupByMolecularProfileId={
+                                                this.store
+                                                    .genericAssayEntitiesGroupedByProfileId
+                                            }
+                                            studyIds={
+                                                this.store
+                                                    .queriedPhysicalStudyIds
+                                            }
+                                            molecularProfilesWithData={
+                                                this.store
+                                                    .molecularProfilesInStudies
+                                            }
+                                            molecularProfilesInStudies={
+                                                this.store
+                                                    .molecularProfilesInStudies
+                                            }
+                                            annotatedCnaCache={
+                                                this.store.annotatedCnaCache
+                                            }
+                                            annotatedMutationCache={
+                                                this.store
+                                                    .annotatedMutationCache
+                                            }
+                                            structuralVariantCache={
+                                                this.store
+                                                    .structuralVariantCache
+                                            }
+                                            studyToMutationMolecularProfile={
+                                                this.store
+                                                    .studyToMutationMolecularProfile
+                                            }
+                                            studyToMolecularProfileDiscreteCna={
+                                                this.store
+                                                    .studyToMolecularProfileDiscreteCna
+                                            }
+                                            clinicalDataCache={
+                                                this.store.clinicalDataCache
+                                            }
+                                            patientKeyToFilteredSamples={
+                                                this.store
+                                                    .patientKeyToFilteredSamples
+                                            }
+                                            numericGeneMolecularDataCache={
+                                                this.store
+                                                    .numericGeneMolecularDataCache
+                                            }
+                                            coverageInformation={
+                                                this.store.coverageInformation
+                                            }
+                                            filteredSamples={
+                                                this.store.selectedSamples
+                                            }
+                                            genesetMolecularDataCache={
+                                                this.store
+                                                    .genesetMolecularDataCache
+                                            }
+                                            genericAssayMolecularDataCache={
+                                                this.store
+                                                    .genericAssayMolecularDataCache
+                                            }
+                                            studyToStructuralVariantMolecularProfile={
+                                                this.store
+                                                    .studyToStructuralVariantMolecularProfile
+                                            }
+                                            driverAnnotationSettings={
+                                                this.store
+                                                    .driverAnnotationSettings
+                                            }
+                                            studyIdToStudy={
+                                                this.store.studyIdToStudy.result
+                                            }
+                                            structuralVariants={
+                                                this.store.structuralVariants
+                                                    .result
+                                            }
+                                            hugoGeneSymbols={
+                                                this.store.allHugoGeneSymbols
+                                                    .result
+                                            }
+                                            selectedGenericAssayEntitiesGroupByMolecularProfileId={
+                                                this.store
+                                                    .selectedGenericAssayEntitiesGroupByMolecularProfileId
+                                            }
+                                            molecularProfileIdToMolecularProfile={
+                                                this.store
+                                                    .molecularProfileIdToMolecularProfile
+                                            }
+                                            urlWrapper={this.urlWrapper}
+                                            hasNoQueriedGenes={true}
+                                            genePanelDataForAllProfiles={
+                                                this.store
+                                                    .genePanelDataForAllProfiles
+                                                    .result
+                                            }
+                                            patients={this.store.patients}
+                                        />
+                                    </MSKTab>
 
                                     {this.resourceTabs.component}
                                     {this.customTabs}
diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts
index e18974f2618..24df9872d29 100644
--- a/src/pages/studyView/StudyViewPageStore.ts
+++ b/src/pages/studyView/StudyViewPageStore.ts
@@ -34,9 +34,14 @@ import {
     DataFilter,
     DataFilterValue,
     DensityPlotBin,
+    DiscreteCopyNumberData,
+    DiscreteCopyNumberFilter,
+    Gene,
     GeneFilter,
     GeneFilterQuery,
     GenePanel,
+    GenePanelData,
+    GenePanelDataMultipleStudyFilter,
     GenericAssayData,
     GenericAssayDataBin,
     GenericAssayDataBinFilter,
@@ -45,11 +50,17 @@ import {
     GenericAssayDataFilter,
     GenericAssayDataMultipleStudyFilter,
     GenericAssayMeta,
+    Geneset,
     GenomicDataBin,
     GenomicDataBinFilter,
     GenomicDataFilter,
+    MolecularDataFilter,
+    MolecularDataMultipleStudyFilter,
     MolecularProfile,
     MolecularProfileFilter,
+    Mutation,
+    MutationFilter,
+    MutationMultipleStudyFilter,
     NumericGeneMolecularData,
     OredPatientTreatmentFilters,
     OredSampleTreatmentFilters,
@@ -61,16 +72,32 @@ import {
     SampleIdentifier,
     SampleMolecularIdentifier,
     SampleTreatmentRow,
+    StructuralVariant,
+    StructuralVariantFilter,
     StructuralVariantFilterQuery,
     StudyViewFilter,
     StudyViewStructuralVariantFilter,
 } from 'cbioportal-ts-api-client';
 import {
+    evaluatePutativeDriverInfo,
+    evaluatePutativeDriverInfoWithHotspots,
+    fetchCnaOncoKbDataForOncoprint,
     fetchCopyNumberSegmentsForSamples,
+    fetchOncoKbDataForOncoprint,
+    filterAndAnnotateMolecularData,
+    filterAndAnnotateMutations,
+    generateDataQueryFilter,
+    getAllGenes,
     getAlterationTypesInOql,
     getDefaultProfilesForOql,
+    getGenomeNexusUrl,
     getSurvivalClinicalAttributesPrefix,
+    IDataQueryFilter,
+    makeGetOncoKbCnaAnnotationForOncoprint,
+    makeGetOncoKbMutationAnnotationForOncoprint,
+    makeIsHotspotForOncoprint,
     MolecularAlterationType_filenameSuffix,
+    ONCOKB_DEFAULT,
 } from 'shared/lib/StoreUtils';
 import { PatientSurvival } from 'shared/model/PatientSurvival';
 import { getPatientSurvivals } from 'pages/resultsView/SurvivalStoreHelper';
@@ -164,6 +191,7 @@ import {
 import { generateDownloadFilenamePrefixByStudies } from 'shared/lib/FilenameUtils';
 import {
     convertToGene1Gene2String,
+    createStructuralVariantQuery,
     parseOQLQuery,
     queryContainsStructVarAlteration,
     unparseOQLQueryLine,
@@ -206,7 +234,7 @@ import { LoadingPhase } from '../groupComparison/GroupComparisonLoading';
 import { sleep, sleepUntil } from '../../shared/lib/TimeUtils';
 import ComplexKeyMap from '../../shared/lib/complexKeyDataStructures/ComplexKeyMap';
 import MobxPromiseCache from 'shared/lib/MobxPromiseCache';
-import { CancerGene } from 'oncokb-ts-api-client';
+import { CancerGene, IndicatorQueryResp } from 'oncokb-ts-api-client';
 
 import { AppStore } from 'AppStore';
 import { getGeneCNAOQL } from 'pages/studyView/TableUtils';
@@ -217,7 +245,11 @@ import {
 } from '../groupComparison/comparisonGroupManager/ComparisonGroupManagerUtils';
 import { IStudyViewScatterPlotData } from './charts/scatterPlot/StudyViewScatterPlotUtils';
 import { StudyViewPageTabKeyEnum } from 'pages/studyView/StudyViewPageTabs';
-import { AlterationTypeConstants, DataTypeConstants } from 'shared/constants';
+import {
+    AlterationTypeConstants,
+    DataTypeConstants,
+    REQUEST_ARG_ENUM,
+} from 'shared/constants';
 import {
     createSurvivalAttributeIdsDict,
     generateStudyViewSurvivalPlotTitle,
@@ -298,6 +330,44 @@ import {
     getAllowedSurvivalClinicalDataFilterId,
     isSurvivalChart,
 } from './charts/survival/StudyViewSurvivalUtils';
+import { allowExpressionCrossStudy } from 'shared/lib/allowExpressionCrossStudy';
+import {
+    CoverageInformation,
+    getCoverageInformation,
+} from 'shared/lib/GenePanelUtils';
+import {
+    createDiscreteCopyNumberDataKey,
+    excludeSpecialMolecularProfiles,
+    ExtendedClinicalAttribute,
+    fetchPatients,
+    getExtendsClinicalAttributesFromCustomData,
+    getGeneAndProfileChunksForRequest,
+    parseGenericAssayGroups,
+} from 'pages/resultsView/ResultsViewPageStoreUtils';
+import {
+    parseSamplesSpecifications,
+    populateSampleSpecificationsFromVirtualStudies,
+} from 'pages/resultsView/ResultsViewPageHelpers';
+import GenericAssayMolecularDataCache from 'shared/cache/GenericAssayMolecularDataCache';
+import GenesetMolecularDataCache from 'shared/cache/GenesetMolecularDataCache';
+import GenesetCache from 'shared/cache/GenesetCache';
+import ClinicalDataCache from 'shared/cache/ClinicalDataCache';
+import { AnnotatedMutation } from 'shared/model/AnnotatedMutation';
+import {
+    IHotspotIndex,
+    indexHotspotsData,
+    IOncoKbData,
+} from 'cbioportal-utils';
+import { fetchHotspotsData } from 'shared/lib/CancerHotspotsUtils';
+import { GenomeNexusAPIInternal } from 'genome-nexus-ts-api-client';
+import eventBus from 'shared/events/eventBus';
+import { SiteError } from 'shared/model/appMisc';
+import { ErrorMessages } from 'shared/errorMessages';
+import { CustomDriverNumericGeneMolecularData } from 'shared/model/CustomDriverNumericGeneMolecularData';
+import {
+    PlotsColoringParam,
+    PlotsSelectionParam,
+} from 'pages/resultsView/ResultsViewURLWrapper';
 
 export const STUDY_VIEW_FILTER_AUTOSUBMIT = 'study_view_filter_autosubmit';
 
@@ -317,6 +387,7 @@ export enum StudyViewPageTabDescriptions {
     CLINICAL_DATA = 'Clinical Data',
     HEATMAPS = 'Heatmaps',
     CN_SEGMENTS = 'CN Segments',
+    PLOTS = 'Plots',
 }
 
 const DEFAULT_CHART_NAME = 'Custom Data';
@@ -349,6 +420,11 @@ export type StudyViewURLQuery = {
     filterValues?: string;
     sharedGroups?: string;
     sharedCustomData?: string;
+    plots_horz_selection?: PlotsSelectionParam;
+    plots_vert_selection?: PlotsSelectionParam;
+    plots_coloring_selection?: PlotsColoringParam;
+    generic_assay_groups?: string;
+    geneset_list?: string;
 };
 
 export type XvsYScatterChart = {
@@ -432,6 +508,22 @@ enum CustomDataTypeEnum {
     NUMERICAL = 'NUMERICAL',
 }
 
+export enum SampleListCategoryType {
+    'w_mut' = 'w_mut',
+    'w_cna' = 'w_cna',
+    'w_mut_cna' = 'w_mut_cna',
+}
+
+export const SampleListCategoryTypeToFullId = {
+    [SampleListCategoryType.w_mut]: 'all_cases_with_mutation_data',
+    [SampleListCategoryType.w_cna]: 'all_cases_with_cna_data',
+    [SampleListCategoryType.w_mut_cna]: 'all_cases_with_mutation_and_cna_data',
+};
+
+export type SamplesSpecificationElement =
+    | { studyId: string; sampleId: string; sampleListId: undefined }
+    | { studyId: string; sampleId: undefined; sampleListId: string };
+
 export class StudyViewPageStore
     implements IAnnotationFilterSettings, ISettingsMenuButtonVisible {
     private reactionDisposers: IReactionDisposer[] = [];
@@ -5227,6 +5319,17 @@ export class StudyViewPageStore
         default: [],
     });
 
+    readonly studyIdToStudy = remoteData(
+        {
+            await: () => [this.queriedPhysicalStudies],
+            invoke: () =>
+                Promise.resolve(
+                    _.keyBy(this.queriedPhysicalStudies.result, x => x.studyId)
+                ),
+        },
+        {}
+    );
+
     readonly queriedSampleIdentifiers = remoteData<SampleIdentifier[]>({
         await: () => [
             this.filteredPhysicalStudies,
@@ -10832,4 +10935,1436 @@ export class StudyViewPageStore
             this.studyIds[0] === 'heme_onc_nsclc_genie_bpc'
         );
     }
+
+    readonly filteredSamplesByDetailedCancerType = remoteData<{
+        [cancerType: string]: Sample[];
+    }>({
+        await: () => [this.selectedSamples, this.cancerStudyAsClinicalData],
+        invoke: () => {
+            let groupedSamples = this.groupSamplesByCancerType(
+                this.cancerStudyAsClinicalData.result,
+                this.selectedSamples.result!,
+                'CANCER_TYPE'
+            );
+            if (_.size(groupedSamples) === 1) {
+                groupedSamples = this.groupSamplesByCancerType(
+                    this.cancerStudyAsClinicalData.result,
+                    this.selectedSamples.result!,
+                    'CANCER_TYPE_DETAILED'
+                );
+            }
+            return Promise.resolve(groupedSamples);
+        },
+    });
+
+    public groupSamplesByCancerType(
+        clinicalDataForSamples: ClinicalData[],
+        samples: Sample[],
+        cancerTypeLevel: 'CANCER_TYPE' | 'CANCER_TYPE_DETAILED'
+    ) {
+        // first generate map of sampleId to it's cancer type
+        const sampleKeyToCancerTypeClinicalDataMap = _.reduce(
+            clinicalDataForSamples,
+            (memo, clinicalData: ClinicalData) => {
+                if (clinicalData.clinicalAttributeId === cancerTypeLevel) {
+                    memo[clinicalData.uniqueSampleKey] = clinicalData.value;
+                }
+
+                // if we were told CANCER_TYPE and we find CANCER_TYPE_DETAILED, then fall back on it. if we encounter
+                // a CANCER_TYPE later, it will override this.
+                if (cancerTypeLevel === 'CANCER_TYPE') {
+                    if (
+                        !memo[clinicalData.uniqueSampleKey] &&
+                        clinicalData.clinicalAttributeId ===
+                            'CANCER_TYPE_DETAILED'
+                    ) {
+                        memo[clinicalData.uniqueSampleKey] = clinicalData.value;
+                    }
+                }
+
+                return memo;
+            },
+            {} as { [uniqueSampleId: string]: string }
+        );
+
+        // now group samples by cancer type
+        let samplesGroupedByCancerType = _.reduce(
+            samples,
+            (memo: { [cancerType: string]: Sample[] }, sample: Sample) => {
+                // if it appears in map, then we have a cancer type
+                if (
+                    sample.uniqueSampleKey in
+                    sampleKeyToCancerTypeClinicalDataMap
+                ) {
+                    memo[
+                        sampleKeyToCancerTypeClinicalDataMap[
+                            sample.uniqueSampleKey
+                        ]
+                    ] =
+                        memo[
+                            sampleKeyToCancerTypeClinicalDataMap[
+                                sample.uniqueSampleKey
+                            ]
+                        ] || [];
+                    memo[
+                        sampleKeyToCancerTypeClinicalDataMap[
+                            sample.uniqueSampleKey
+                        ]
+                    ].push(sample);
+                } else {
+                    // TODO: we need to fall back to study cancer type
+                }
+                return memo;
+            },
+            {} as { [cancerType: string]: Sample[] }
+        );
+
+        return samplesGroupedByCancerType;
+        //
+    }
+
+    readonly allGenes = remoteData<Gene[]>({
+        invoke: () => {
+            return getAllGenes();
+        },
+    });
+
+    readonly plotsSelectedGenes = remoteData<Gene[]>({
+        invoke: () => {
+            let entrezIds: string[] = [];
+            // gene selected in horz axis
+            if (
+                this.urlWrapper.query.plots_horz_selection?.selectedGeneOption
+            ) {
+                entrezIds.push(
+                    this.urlWrapper.query.plots_horz_selection
+                        .selectedGeneOption
+                );
+            }
+            // gene selected in vert axis
+            if (
+                this.urlWrapper.query.plots_vert_selection?.selectedGeneOption
+            ) {
+                entrezIds.push(
+                    this.urlWrapper.query.plots_vert_selection
+                        .selectedGeneOption
+                );
+            }
+            // gene selected in color menu
+            if (
+                this.urlWrapper.query.plots_coloring_selection
+                    ?.selectedOption &&
+                this.urlWrapper.query.plots_coloring_selection.selectedOption.match(
+                    '^[0-9]*'
+                )
+            ) {
+                // extract entrezGeneId from plot coloring selection string
+                let selectedColoringGene = this.urlWrapper.query.plots_coloring_selection.selectedOption.match(
+                    '^[0-9]*'
+                )![0];
+                entrezIds.push(selectedColoringGene);
+            }
+            if (entrezIds.length > 0) {
+                return client.fetchGenesUsingPOST({
+                    geneIdType: 'ENTREZ_GENE_ID',
+                    geneIds: entrezIds,
+                });
+            }
+            return Promise.resolve([]);
+        },
+    });
+
+    readonly entrezGeneIdToGeneAll = remoteData<{
+        [entrezGeneId: string]: Gene;
+    }>({
+        await: () => [this.allGenes],
+        invoke: () => {
+            // build reference gene map
+            return Promise.resolve(
+                _.keyBy(this.allGenes.result!, g => g.entrezGeneId)
+            );
+        },
+    });
+
+    readonly allHugoGeneSymbols = remoteData<string[]>({
+        await: () => [this.allGenes],
+        invoke: () => {
+            // build reference gene map
+            return Promise.resolve(
+                this.allGenes.result!.map(g => g.hugoGeneSymbol)
+            );
+        },
+        default: [],
+    });
+
+    @computed get selectedGenericAssayEntitiesGroupByMolecularProfileId() {
+        return parseGenericAssayGroups(
+            this.urlWrapper.query.generic_assay_groups || ''
+        );
+    }
+
+    readonly molecularProfileIdSuffixToMolecularProfiles = remoteData<{
+        [molecularProfileIdSuffix: string]: MolecularProfile[];
+    }>(
+        {
+            await: () => [this.molecularProfilesInStudies],
+            invoke: () => {
+                return Promise.resolve(
+                    _.groupBy(
+                        this.molecularProfilesInStudies.result,
+                        molecularProfile =>
+                            getSuffixOfMolecularProfile(molecularProfile)
+                    )
+                );
+            },
+        },
+        {}
+    );
+
+    readonly molecularProfileIdToMolecularProfile = remoteData<{
+        [molecularProfileId: string]: MolecularProfile;
+    }>(
+        {
+            await: () => [this.molecularProfilesInStudies],
+            invoke: () => {
+                return Promise.resolve(
+                    this.molecularProfilesInStudies.result.reduce(
+                        (
+                            map: {
+                                [molecularProfileId: string]: MolecularProfile;
+                            },
+                            next: MolecularProfile
+                        ) => {
+                            map[next.molecularProfileId] = next;
+                            return map;
+                        },
+                        {}
+                    )
+                );
+            },
+        },
+        {}
+    );
+
+    readonly molecularProfilesInStudies = remoteData<MolecularProfile[]>(
+        {
+            await: () => [this.queriedPhysicalStudyIds],
+            invoke: async () => {
+                let profiles = await client.fetchMolecularProfilesUsingPOST({
+                    molecularProfileFilter: {
+                        studyIds: this.queriedPhysicalStudyIds.result,
+                    } as MolecularProfileFilter,
+                });
+
+                // expression profiles are not allowed
+                // under some circumstances
+                if (
+                    allowExpressionCrossStudy(
+                        this.queriedPhysicalStudies.result,
+                        getServerConfig().enable_cross_study_expression,
+                        false
+                    )
+                ) {
+                    return profiles;
+                } else {
+                    return profiles.filter(
+                        p =>
+                            ![
+                                AlterationTypeConstants.MRNA_EXPRESSION,
+                                AlterationTypeConstants.MICRO_RNA_EXPRESSION,
+                                AlterationTypeConstants.PROTEIN_LEVEL,
+                                AlterationTypeConstants.RNA_EXPRESSION,
+                                AlterationTypeConstants.MICRO_RNA_EXPRESSION,
+                            ].includes(p.molecularAlterationType)
+                    );
+                }
+            },
+        },
+        []
+    );
+
+    readonly studyToMutationMolecularProfile = remoteData<{
+        [studyId: string]: MolecularProfile;
+    }>(
+        {
+            await: () => [this.mutationProfiles],
+            invoke: () => {
+                return Promise.resolve(
+                    _.keyBy(
+                        this.mutationProfiles.result,
+                        (profile: MolecularProfile) => profile.studyId
+                    )
+                );
+            },
+        },
+        {}
+    );
+
+    readonly studyToMolecularProfileDiscreteCna = remoteData<{
+        [studyId: string]: MolecularProfile;
+    }>(
+        {
+            await: () => [this.molecularProfilesInStudies],
+            invoke: async () => {
+                const ret: { [studyId: string]: MolecularProfile } = {};
+                for (const molecularProfile of this.molecularProfilesInStudies
+                    .result) {
+                    if (
+                        molecularProfile.datatype ===
+                            DataTypeConstants.DISCRETE &&
+                        molecularProfile.molecularAlterationType ===
+                            AlterationTypeConstants.COPY_NUMBER_ALTERATION
+                    ) {
+                        ret[molecularProfile.studyId] = molecularProfile;
+                    }
+                }
+                return ret;
+            },
+        },
+        {}
+    );
+
+    readonly studyToStructuralVariantMolecularProfile = remoteData<{
+        [studyId: string]: MolecularProfile;
+    }>(
+        {
+            await: () => [this.structuralVariantProfiles],
+            invoke: () => {
+                return Promise.resolve(
+                    _.keyBy(
+                        this.structuralVariantProfiles.result,
+                        (profile: MolecularProfile) => profile.studyId
+                    )
+                );
+            },
+        },
+        {}
+    );
+
+    readonly patientKeyToFilteredSamples = remoteData({
+        await: () => [this.selectedSamples],
+        invoke: () => {
+            return Promise.resolve(
+                _.groupBy(
+                    this.selectedSamples.result!,
+                    sample => sample.uniquePatientKey
+                )
+            );
+        },
+    });
+
+    readonly structuralVariants = remoteData<StructuralVariant[]>({
+        await: () => [
+            this.plotsSelectedGenes,
+            this.samples,
+            this.studyToStructuralVariantMolecularProfile,
+            this.entrezGeneIdToGeneAll,
+        ],
+        invoke: async () => {
+            if (
+                _.isEmpty(
+                    this.studyToStructuralVariantMolecularProfile.result
+                ) ||
+                _.isEmpty(this.plotsSelectedGenes.result)
+            ) {
+                return [];
+            }
+            const studyIdToProfileMap = this
+                .studyToStructuralVariantMolecularProfile.result;
+
+            const sampleMolecularIdentifiers = this.samples.result.reduce(
+                (memo, sample: Sample) => {
+                    if (sample.studyId in studyIdToProfileMap) {
+                        memo.push({
+                            molecularProfileId:
+                                studyIdToProfileMap[sample.studyId]
+                                    .molecularProfileId,
+                            sampleId: sample.sampleId,
+                        });
+                    }
+                    return memo;
+                },
+                [] as StructuralVariantFilter['sampleMolecularIdentifiers']
+            );
+
+            // Filters can be an empty list. When all selected samples are coming from studies that do not have
+            // structural variant profile in this case, we should not fetch structural variant data.
+            if (_.isEmpty(sampleMolecularIdentifiers)) {
+                return [];
+            } else {
+                // Set all SVs that are queried at the gene level.
+                // The gene1::gene2 orientation does not come into play here.
+                const entrezGeneIds = _.map(
+                    this.plotsSelectedGenes.result,
+                    (gene: Gene) => gene.entrezGeneId
+                );
+                // // Set all SVs that are queried at the gene1::gene2 orientation level.
+                // const structuralVariantQueries = this.structVarQueries.map(sv =>
+                //     createStructuralVariantQuery(sv, this.plotsSelectedGenes.result!)
+                // );
+
+                return await internalClient.fetchStructuralVariantsUsingPOST({
+                    structuralVariantFilter: {
+                        entrezGeneIds,
+                        structuralVariantQueries: [],
+                        sampleMolecularIdentifiers,
+                        molecularProfileIds: [],
+                    },
+                });
+            }
+        },
+    });
+
+    readonly coverageInformation = remoteData<CoverageInformation>({
+        await: () => [
+            this.genePanelDataForAllProfiles,
+            this.sampleSetByKey,
+            this.patients,
+            this.plotsSelectedGenes,
+        ],
+        invoke: () =>
+            getCoverageInformation(
+                this.genePanelDataForAllProfiles.result!,
+                this.sampleSetByKey.result!,
+                this.patients.result!,
+                this.plotsSelectedGenes.result!
+            ),
+    });
+
+    readonly patients = remoteData({
+        await: () => [this.samples],
+        invoke: () => fetchPatients(this.samples.result!),
+        default: [],
+    });
+
+    readonly genePanelDataForAllProfiles = remoteData<GenePanelData[]>({
+        // fetch all gene panel data for profiles
+        // We do it this way - fetch all data for profiles, then filter based on samples -
+        //  because
+        //  (1) this means sending less data as parameters
+        //  (2) this means the requests can be cached on the server based on the molecular profile id
+        //  (3) We can initiate the gene panel data call before the samples call completes, thus
+        //      putting more response waiting time in parallel
+        await: () => [this.molecularProfilesInStudies],
+        invoke: () =>
+            client.fetchGenePanelDataInMultipleMolecularProfilesUsingPOST({
+                genePanelDataMultipleStudyFilter: {
+                    molecularProfileIds: this.molecularProfilesInStudies.result.map(
+                        p => p.molecularProfileId
+                    ),
+                } as GenePanelDataMultipleStudyFilter,
+            }),
+    });
+
+    readonly mutations_preload = remoteData<Mutation[]>({
+        // fetch all mutation data for profiles
+        // We do it this way - fetch all data for profiles, then filter based on samples -
+        //  because
+        //  (1) this means sending less data as parameters
+        //  (2) this means the requests can be cached on the server based on the molecular profile id
+        //  (3) We can initiate the mutations call before the samples call completes, thus
+        //      putting more response waiting time in parallel
+        await: () => [this.plotsSelectedGenes, this.mutationProfiles],
+        invoke: () => {
+            if (
+                this.plotsSelectedGenes.result!.length === 0 ||
+                this.mutationProfiles.result!.length === 0
+            ) {
+                return Promise.resolve([]);
+            }
+
+            return client.fetchMutationsInMultipleMolecularProfilesUsingPOST({
+                projection: REQUEST_ARG_ENUM.PROJECTION_DETAILED,
+                mutationMultipleStudyFilter: {
+                    entrezGeneIds: this.plotsSelectedGenes.result!.map(
+                        g => g.entrezGeneId
+                    ),
+                    molecularProfileIds: this.mutationProfiles.result!.map(
+                        p => p.molecularProfileId
+                    ),
+                } as MutationMultipleStudyFilter,
+            });
+        },
+    });
+
+    readonly mutations = remoteData<Mutation[]>({
+        await: () => [this.mutations_preload, this.sampleSetByKey],
+        invoke: () => {
+            const sampleKeys = this.sampleSetByKey.result!;
+            return Promise.resolve(
+                this.mutations_preload.result!.filter(
+                    m => m.uniqueSampleKey in sampleKeys
+                )
+            );
+        },
+    });
+
+    readonly genericAssayMolecularDataCache = remoteData({
+        await: () => [this.molecularProfileIdToDataQueryFilter],
+        invoke: () =>
+            Promise.resolve(
+                new GenericAssayMolecularDataCache(
+                    this.molecularProfileIdToDataQueryFilter.result!
+                )
+            ),
+    });
+
+    readonly genesetMolecularDataCache = remoteData({
+        await: () => [this.molecularProfileIdToDataQueryFilter],
+        invoke: () =>
+            Promise.resolve(
+                new GenesetMolecularDataCache(
+                    this.molecularProfileIdToDataQueryFilter.result!
+                )
+            ),
+    });
+
+    readonly molecularProfileIdToDataQueryFilter = remoteData<{
+        [molecularProfileId: string]: IDataQueryFilter;
+    }>({
+        await: () => [
+            this.molecularProfilesInStudies,
+            this.studyToDataQueryFilter,
+        ],
+        invoke: () => {
+            const ret: { [molecularProfileId: string]: IDataQueryFilter } = {};
+            for (const molecularProfile of this.molecularProfilesInStudies
+                .result!) {
+                ret[
+                    molecularProfile.molecularProfileId
+                ] = this.studyToDataQueryFilter.result![
+                    molecularProfile.studyId
+                ];
+            }
+            return Promise.resolve(ret);
+        },
+        default: {},
+    });
+
+    readonly studyToDataQueryFilter = remoteData<{
+        [studyId: string]: IDataQueryFilter;
+    }>(
+        {
+            await: () => [
+                this.studyToCustomSampleList,
+                this.studyToSampleListId,
+            ],
+            invoke: () => {
+                const studies = this.studyIds;
+                const ret: { [studyId: string]: IDataQueryFilter } = {};
+                for (const studyId of studies) {
+                    ret[studyId] = generateDataQueryFilter(
+                        this.studyToSampleListId.result![studyId],
+                        this.studyToCustomSampleList.result![studyId]
+                    );
+                }
+                return Promise.resolve(ret);
+            },
+        },
+        {}
+    );
+
+    readonly studyToCustomSampleList = remoteData<{
+        [studyId: string]: string[];
+    }>(
+        {
+            await: () => [this.samplesSpecification],
+            invoke: () => {
+                const ret: {
+                    [studyId: string]: string[];
+                } = {};
+                for (const sampleSpec of this.samplesSpecification.result!) {
+                    if (sampleSpec.sampleId) {
+                        // add sample id to study
+                        ret[sampleSpec.studyId] = ret[sampleSpec.studyId] || [];
+                        ret[sampleSpec.studyId].push(sampleSpec.sampleId);
+                    }
+                }
+                return Promise.resolve(ret);
+            },
+        },
+        {}
+    );
+
+    @computed get sampleListCategory(): SampleListCategoryType | undefined {
+        if (
+            [
+                SampleListCategoryType.w_mut,
+                SampleListCategoryType.w_cna,
+                SampleListCategoryType.w_mut_cna,
+            ].includes((this.studyIds[0] + '_all') as any)
+        ) {
+            return (this.studyIds[0] + '_all') as SampleListCategoryType;
+        } else {
+            return undefined;
+        }
+    }
+
+    @computed get samplesSpecificationParams() {
+        const unknownQueriedIdsMap = stringListToSet(
+            this.unknownQueriedIds.result
+        );
+        return parseSamplesSpecifications(
+            _.map(this.selectedSamples.result, sample => {
+                return sample.studyId + ':' + sample.sampleId;
+            }).join('+'),
+            undefined,
+            this.studyIds[0] + '_all',
+            this.studyIds.filter(studyId => !unknownQueriedIdsMap[studyId])
+        );
+    }
+
+    readonly samplesSpecification = remoteData({
+        await: () => [this.filteredVirtualStudies],
+        invoke: async () => {
+            // is this a sample list category query?
+            // if YES, we need to derive the sample lists by:
+            // 1. looking up all sample lists in selected studies
+            // 2. using those with matching category
+            if (!this.sampleListCategory) {
+                if (this.filteredVirtualStudies.result!.length > 0) {
+                    return populateSampleSpecificationsFromVirtualStudies(
+                        this.samplesSpecificationParams,
+                        this.filteredVirtualStudies.result!
+                    );
+                } else {
+                    return this.samplesSpecificationParams;
+                }
+            } else {
+                // would be nice to have an endpoint that would return multiple sample lists
+                // but this will only ever happen one for each study selected (and in queries where a sample list is specified)
+                let samplesSpecifications = [];
+                // get sample specifications from physical studies if we are querying virtual study
+                if (this.filteredVirtualStudies.result!.length > 0) {
+                    samplesSpecifications = populateSampleSpecificationsFromVirtualStudies(
+                        this.samplesSpecificationParams,
+                        this.filteredVirtualStudies.result!
+                    );
+                } else {
+                    samplesSpecifications = this.samplesSpecificationParams;
+                }
+                // get unique study ids to reduce the API requests
+                const uniqueStudyIds = _.chain(samplesSpecifications)
+                    .map(specification => specification.studyId)
+                    .uniq()
+                    .value();
+                const allSampleLists = await Promise.all(
+                    uniqueStudyIds.map(studyId => {
+                        return client.getAllSampleListsInStudyUsingGET({
+                            studyId: studyId,
+                            projection: REQUEST_ARG_ENUM.PROJECTION_SUMMARY,
+                        });
+                    })
+                );
+
+                const category =
+                    SampleListCategoryTypeToFullId[this.sampleListCategory!];
+                const specs = allSampleLists.reduce(
+                    (
+                        aggregator: SamplesSpecificationElement[],
+                        sampleLists
+                    ) => {
+                        //find the sample list matching the selected category using the map from shortname to full category name :(
+                        const matchingList = _.find(
+                            sampleLists,
+                            list => list.category === category
+                        );
+                        if (matchingList) {
+                            aggregator.push({
+                                studyId: matchingList.studyId,
+                                sampleListId: matchingList.sampleListId,
+                                sampleId: undefined,
+                            } as SamplesSpecificationElement);
+                        }
+                        return aggregator;
+                    },
+                    []
+                );
+
+                return specs;
+            }
+        },
+    });
+
+    readonly studyToSampleListId = remoteData<{ [studyId: string]: string }>({
+        await: () => [this.samplesSpecification],
+        invoke: async () => {
+            return this.samplesSpecification.result!.reduce((map, next) => {
+                if (next.sampleListId) {
+                    map[next.studyId] = next.sampleListId;
+                }
+                return map;
+            }, {} as { [studyId: string]: string });
+        },
+    });
+
+    readonly genesetCache = new GenesetCache();
+
+    @computed get genesetIds() {
+        return this.urlWrapper.query.geneset_list &&
+            this.urlWrapper.query.geneset_list.trim().length
+            ? this.urlWrapper.query.geneset_list.trim().split(/\s+/)
+            : [];
+    }
+
+    readonly genesets = remoteData<Geneset[]>({
+        invoke: () => {
+            if (this.genesetIds && this.genesetIds.length > 0) {
+                return internalClient.fetchGenesetsUsingPOST({
+                    genesetIds: this.genesetIds.slice(),
+                });
+            } else {
+                return Promise.resolve([]);
+            }
+        },
+        onResult: (genesets: Geneset[]) => {
+            this.genesetCache.addData(genesets);
+        },
+    });
+
+    public structuralVariantCache = new MobxPromiseCache<
+        { entrezGeneId: number },
+        StructuralVariant[]
+    >(q => ({
+        await: () => [
+            this.studyToStructuralVariantMolecularProfile,
+            this.studyToDataQueryFilter,
+        ],
+        invoke: async () => {
+            const studyIdToProfileMap = this
+                .studyToStructuralVariantMolecularProfile.result!;
+
+            if (_.isEmpty(studyIdToProfileMap)) {
+                return Promise.resolve([]);
+            }
+
+            const filters = this.samples.result.reduce(
+                (memo, sample: Sample) => {
+                    if (sample.studyId in studyIdToProfileMap) {
+                        memo.push({
+                            molecularProfileId:
+                                studyIdToProfileMap[sample.studyId]
+                                    .molecularProfileId,
+                            sampleId: sample.sampleId,
+                        });
+                    }
+                    return memo;
+                },
+                [] as StructuralVariantFilter['sampleMolecularIdentifiers']
+            );
+
+            if (_.isEmpty(filters)) {
+                return [];
+            } else {
+                return internalClient.fetchStructuralVariantsUsingPOST({
+                    structuralVariantFilter: {
+                        entrezGeneIds: [q.entrezGeneId],
+                        sampleMolecularIdentifiers: filters,
+                    } as StructuralVariantFilter,
+                });
+            }
+        },
+    }));
+
+    readonly filteredSampleKeyToSample = remoteData({
+        await: () => [this.selectedSamples],
+        invoke: () =>
+            Promise.resolve(
+                _.keyBy(this.selectedSamples.result!, s => s.uniqueSampleKey)
+            ),
+    });
+
+    readonly filteredPatientKeyToPatient = remoteData({
+        invoke: () =>
+            Promise.resolve(
+                _.keyBy(this.selectedPatients, p => p.uniquePatientKey)
+            ),
+    });
+
+    readonly clinicalAttributes_customCharts = remoteData({
+        await: () => [this.sampleMap],
+        invoke: async () => {
+            let ret: ExtendedClinicalAttribute[] = [];
+            if (this.appStore.isLoggedIn) {
+                try {
+                    const unknownQueriedIdsMap = stringListToSet(
+                        this.unknownQueriedIds.result
+                    );
+                    //Add custom data from user profile
+                    const customChartSessions = await sessionServiceClient.getCustomDataForStudies(
+                        this.studyIds.filter(
+                            studyId => !unknownQueriedIdsMap[studyId]
+                        )
+                    );
+
+                    ret = getExtendsClinicalAttributesFromCustomData(
+                        customChartSessions,
+                        this.sampleMap.result!
+                    );
+                } catch (e) {}
+            }
+            return ret;
+        },
+    });
+
+    readonly sampleMap = remoteData({
+        await: () => [this.samples],
+        invoke: () => {
+            return Promise.resolve(
+                ComplexKeyMap.from(this.samples.result!, s => ({
+                    studyId: s.studyId,
+                    sampleId: s.sampleId,
+                }))
+            );
+        },
+    });
+
+    public clinicalDataCache = new ClinicalDataCache(
+        this.samples,
+        this.patients,
+        this.studyToMutationMolecularProfile,
+        this.everyStudyIdToStudy,
+        this.coverageInformation,
+        this.filteredSampleKeyToSample,
+        this.filteredPatientKeyToPatient,
+        this.clinicalAttributes_customCharts
+    );
+
+    private _numericGeneMolecularDataCache = new MobxPromiseCache<
+        { entrezGeneId: number; molecularProfileId: string },
+        NumericGeneMolecularData[]
+    >(q => ({
+        await: () => [this.molecularProfileIdToDataQueryFilter],
+        invoke: () => {
+            const dqf = this.molecularProfileIdToDataQueryFilter.result![
+                q.molecularProfileId
+            ];
+            // it's possible that sampleIds is empty for a given profile
+            const hasSampleSpec =
+                dqf &&
+                ((dqf.sampleIds && dqf.sampleIds.length) || dqf.sampleListId);
+            if (hasSampleSpec) {
+                return client.fetchAllMolecularDataInMolecularProfileUsingPOST({
+                    molecularProfileId: q.molecularProfileId,
+                    molecularDataFilter: {
+                        entrezGeneIds: [q.entrezGeneId],
+                        ...dqf,
+                    } as MolecularDataFilter,
+                });
+            } else {
+                return Promise.resolve([]);
+            }
+        },
+    }));
+    public numericGeneMolecularDataCache = new MobxPromiseCache<
+        { entrezGeneId: number; molecularProfileId: string },
+        NumericGeneMolecularData[]
+    >(q => ({
+        await: () => [
+            this._numericGeneMolecularDataCache.get(q),
+            this.filteredSampleKeyToSample,
+        ],
+        invoke: () => {
+            const data = this._numericGeneMolecularDataCache.get(q).result!;
+            const sampleMap = this.filteredSampleKeyToSample.result!;
+            return Promise.resolve(
+                data.filter(d => d.uniqueSampleKey in sampleMap)
+            );
+        },
+    }));
+
+    public annotatedCnaCache = new MobxPromiseCache<
+        { entrezGeneId: number },
+        CustomDriverNumericGeneMolecularData[]
+    >(q => ({
+        await: () =>
+            this.numericGeneMolecularDataCache.await(
+                [
+                    this.studyToMolecularProfileDiscreteCna,
+                    this.getDiscreteCNAPutativeDriverInfo,
+                    this.entrezGeneIdToGeneAll,
+                ],
+                studyToMolecularProfileDiscrete => {
+                    return _.values(studyToMolecularProfileDiscrete).map(p => ({
+                        entrezGeneId: q.entrezGeneId,
+                        molecularProfileId: p.molecularProfileId,
+                    }));
+                }
+            ),
+        invoke: () => {
+            const cnaData = _.flatten(
+                this.numericGeneMolecularDataCache
+                    .getAll(
+                        _.values(
+                            this.studyToMolecularProfileDiscreteCna.result!
+                        ).map(p => ({
+                            entrezGeneId: q.entrezGeneId,
+                            molecularProfileId: p.molecularProfileId,
+                        }))
+                    )
+                    .map(p => p.result!)
+            ) as CustomDriverNumericGeneMolecularData[];
+            const filteredAndAnnotatedReport = filterAndAnnotateMolecularData(
+                cnaData,
+                this.getDiscreteCNAPutativeDriverInfo.result!,
+                this.entrezGeneIdToGeneAll.result!
+            );
+            const data = filteredAndAnnotatedReport.data.concat(
+                filteredAndAnnotatedReport.vus
+            );
+
+            return Promise.resolve(
+                filteredAndAnnotatedReport.data.concat(
+                    filteredAndAnnotatedReport.vus
+                )
+            );
+        },
+    }));
+
+    readonly getDiscreteCNAPutativeDriverInfo = remoteData({
+        await: () => {
+            const toAwait = [];
+            if (this.driverAnnotationSettings.oncoKb) {
+                toAwait.push(this.getOncoKbCnaAnnotationForOncoprint);
+            }
+            return toAwait;
+        },
+        invoke: () => {
+            return Promise.resolve(
+                (
+                    cnaDatum: CustomDriverNumericGeneMolecularData
+                ): {
+                    oncoKb: string;
+                    customDriverBinary: boolean;
+                    customDriverTier?: string | undefined;
+                } => {
+                    const getOncoKBAnnotationFunc = this
+                        .getOncoKbCnaAnnotationForOncoprint.result!;
+                    const oncoKbDatum:
+                        | IndicatorQueryResp
+                        | undefined
+                        | null
+                        | false =
+                        this.driverAnnotationSettings.oncoKb &&
+                        getOncoKBAnnotationFunc &&
+                        !(getOncoKBAnnotationFunc instanceof Error) &&
+                        getOncoKBAnnotationFunc(cnaDatum);
+
+                    // Note: custom driver annotations are part of the incoming datum
+                    return evaluatePutativeDriverInfo(
+                        cnaDatum,
+                        oncoKbDatum,
+                        this.driverAnnotationSettings.customBinary,
+                        this.driverAnnotationSettings.driverTiers
+                    );
+                }
+            );
+        },
+    });
+
+    readonly getOncoKbCnaAnnotationForOncoprint = remoteData<
+        | Error
+        | ((data: NumericGeneMolecularData) => IndicatorQueryResp | undefined)
+    >({
+        await: () => [this.cnaOncoKbDataForOncoprint],
+        invoke: () =>
+            makeGetOncoKbCnaAnnotationForOncoprint(
+                this.cnaOncoKbDataForOncoprint,
+                this.driverAnnotationSettings.oncoKb
+            ),
+    });
+
+    //we need seperate oncokb data because oncoprint requires onkb queries across cancertype
+    //mutations tab the opposite
+    readonly cnaOncoKbDataForOncoprint = remoteData<IOncoKbData | Error>(
+        {
+            await: () => [
+                this.oncoKbAnnotatedGenes,
+                this.discreteCNAMolecularData,
+            ],
+            invoke: async () =>
+                fetchCnaOncoKbDataForOncoprint(
+                    this.oncoKbAnnotatedGenes,
+                    this.discreteCNAMolecularData
+                ),
+        },
+        ONCOKB_DEFAULT
+    );
+
+    // Isolate discrete CNA data from other NumericMolecularData
+    // and add the custom driver annotations to data points
+    readonly discreteCNAMolecularData = remoteData<
+        CustomDriverNumericGeneMolecularData[]
+    >({
+        await: () => [this.discreteCopyNumberAlterations, this.molecularData],
+        invoke: () => {
+            const cnaData = _.filter(
+                this.molecularData.result as any,
+                (d: any) => {
+                    return _.includes(
+                        this.cnaMolecularProfileIds,
+                        d.molecularProfileId
+                    );
+                }
+            );
+            _.forEach(cnaData, (d: any) => {
+                // Lookup the DiscreteCopyNumberData datum that
+                // holds the custom driver annotation.
+                const discreteCopyNumberDatumKey = createDiscreteCopyNumberDataKey(
+                    d
+                );
+                const discreteCopyNumberDatum =
+                    discreteCopyNumberDatumKey in
+                    this.sampleIdAndEntrezIdToDiscreteCopyNumberData
+                        ? this.sampleIdAndEntrezIdToDiscreteCopyNumberData[
+                              discreteCopyNumberDatumKey
+                          ]
+                        : undefined;
+
+                d.driverFilter = discreteCopyNumberDatum
+                    ? discreteCopyNumberDatum.driverFilter
+                    : '';
+                d.driverFilterAnnotation = discreteCopyNumberDatum
+                    ? discreteCopyNumberDatum.driverFilterAnnotation
+                    : '';
+                d.driverTiersFilter = discreteCopyNumberDatum
+                    ? discreteCopyNumberDatum.driverTiersFilter
+                    : '';
+                d.driverTiersFilterAnnotation = discreteCopyNumberDatum
+                    ? discreteCopyNumberDatum.driverTiersFilterAnnotation
+                    : '';
+            });
+            return Promise.resolve(
+                cnaData as CustomDriverNumericGeneMolecularData[]
+            );
+        },
+    });
+
+    readonly discreteCopyNumberAlterations = remoteData<
+        DiscreteCopyNumberData[]
+    >({
+        await: () => [
+            this.discreteCopyNumberAlterations_preload,
+            this.sampleSetByKey,
+        ],
+        invoke: async () => {
+            if (
+                this.discreteCopyNumberAlterations_preload.result!.length == 0
+            ) {
+                return [];
+            }
+
+            return Promise.resolve(
+                this.discreteCopyNumberAlterations_preload.result!.filter(
+                    dcna => {
+                        return (
+                            dcna.uniqueSampleKey in this.sampleSetByKey.result!
+                        );
+                    }
+                )
+            );
+        },
+    });
+
+    // we want to load dcna using sample list id (instead of list of samples)
+    // and then filter down to those contained in actually queried samples
+    // this is an optimization that allows us to fire these calls earlier
+    // and to make cache items finite (by "all" sample list id)
+    readonly discreteCopyNumberAlterations_preload = remoteData<
+        DiscreteCopyNumberData[]
+    >({
+        await: () => [
+            this.plotsSelectedGenes,
+            this.studyToMolecularProfileDiscreteCna,
+        ],
+        invoke: async () => {
+            if (
+                this.cnaMolecularProfileIds.length === 0 ||
+                this.plotsSelectedGenes.result!.length === 0
+            ) {
+                return [];
+            }
+
+            const entrezGeneIds = _.map(
+                this.plotsSelectedGenes.result!,
+                (gene: Gene) => gene.entrezGeneId
+            );
+
+            const promises = _.map(
+                this.studyToMolecularProfileDiscreteCna.result,
+                (cnaMolecularProfile, studyId) => {
+                    return client.fetchDiscreteCopyNumbersInMolecularProfileUsingPOST(
+                        {
+                            discreteCopyNumberEventType: 'HOMDEL_AND_AMP',
+                            discreteCopyNumberFilter: {
+                                entrezGeneIds,
+                                sampleListId: `${studyId}_all`,
+                            } as DiscreteCopyNumberFilter,
+                            molecularProfileId:
+                                cnaMolecularProfile.molecularProfileId,
+                            projection: 'DETAILED',
+                        }
+                    );
+                }
+            );
+
+            return Promise.all(promises).then((cnaData: any[]) =>
+                _.flattenDeep(cnaData)
+            );
+        },
+    });
+
+    @computed get cnaMolecularProfileIds() {
+        const profiles = this.cnaProfiles.isComplete
+            ? this.cnaProfiles.result
+            : [];
+        const profileIds = _.map(
+            profiles,
+            (p: MolecularProfile) => p.molecularProfileId
+        );
+        return profileIds;
+    }
+
+    /**
+     * All molecular data that is 'special', i.e. not a:
+     * - structural variant
+     * - mutation
+     * - generic essay
+     * See also {@link excludeSpecialMolecularProfiles}
+     */
+    readonly molecularData = remoteData<NumericGeneMolecularData[]>({
+        await: () => [
+            this.sampleSetByKey,
+            this.molecularData_preload,
+            this.molecularProfiles,
+            this.samples,
+        ],
+        invoke: () => {
+            const sampleKeys = this.sampleSetByKey.result!;
+            return Promise.resolve(
+                this.molecularData_preload.result.filter(
+                    m => m.uniqueSampleKey in sampleKeys
+                )
+            );
+        },
+    });
+
+    // loading molecular data based on profileId (instead of individual samples) provides
+    // two optimizations.
+    // 1. we can load this data before we know samples
+    // 2. backend can cache based on finite set of profiles
+    // we then have to filter this using samples, which can be loaded concurrently instead of serially
+    readonly molecularData_preload = remoteData<NumericGeneMolecularData[]>({
+        await: () => [
+            this.plotsSelectedGenes,
+            this.displayedStudies,
+            this.molecularProfiles,
+        ],
+        invoke: async () => {
+            // we get mutations with mutations endpoint, structural variants and fusions with structural variant endpoint, generic assay with generic assay endpoint.
+            // filter out mutation genetic profile and structural variant profiles and generic assay profiles
+            const profilesWithoutMutationProfile = excludeSpecialMolecularProfiles(
+                this.molecularProfiles.result!
+            );
+            const genes = this.plotsSelectedGenes.result;
+
+            if (
+                profilesWithoutMutationProfile.length &&
+                genes != undefined &&
+                genes.length
+            ) {
+                const molecularProfileIds = profilesWithoutMutationProfile.map(
+                    p => p.molecularProfileId
+                );
+                const numSamples = _.sumBy(
+                    this.displayedStudies.result!,
+                    s => s.allSampleCount
+                );
+
+                // if size of response is too big (around 1.6 million), the request seems to fail. This is a conservative limit
+                const maximumDataPointsPerRequest = 1500000;
+
+                const {
+                    geneChunks,
+                    profileChunks,
+                } = getGeneAndProfileChunksForRequest(
+                    maximumDataPointsPerRequest,
+                    numSamples,
+                    genes,
+                    molecularProfileIds
+                );
+
+                const dataPromises: Promise<NumericGeneMolecularData[]>[] = [];
+
+                geneChunks.forEach(geneChunk => {
+                    profileChunks.forEach(profileChunk => {
+                        const molecularDataMultipleStudyFilter = {
+                            entrezGeneIds: geneChunk.map(g => g.entrezGeneId),
+                            molecularProfileIds: profileChunk,
+                        } as MolecularDataMultipleStudyFilter;
+
+                        dataPromises.push(
+                            client.fetchMolecularDataInMultipleMolecularProfilesUsingPOST(
+                                {
+                                    projection:
+                                        REQUEST_ARG_ENUM.PROJECTION_DETAILED,
+                                    molecularDataMultipleStudyFilter,
+                                }
+                            )
+                        );
+                    });
+                });
+
+                const allData = await Promise.all(dataPromises);
+                return _.flatten(allData);
+            }
+
+            return [];
+        },
+        default: [],
+    });
+
+    @computed get sampleIdAndEntrezIdToDiscreteCopyNumberData() {
+        return _.keyBy(
+            this.discreteCopyNumberAlterations.result,
+            (d: DiscreteCopyNumberData) => createDiscreteCopyNumberDataKey(d)
+        );
+    }
+
+    public annotatedMutationCache = new MobxPromiseCache<
+        { entrezGeneId: number },
+        AnnotatedMutation[]
+    >(q => ({
+        await: () => [
+            this.mutationCache.get(q),
+            this.getMutationPutativeDriverInfo,
+            this.entrezGeneIdToGeneAll,
+        ],
+        invoke: () => {
+            const filteredAndAnnotatedReport = filterAndAnnotateMutations(
+                this.mutationCache.get(q).result!,
+                this.getMutationPutativeDriverInfo.result!,
+                this.entrezGeneIdToGeneAll.result!
+            );
+            const data = filteredAndAnnotatedReport.data
+                .concat(filteredAndAnnotatedReport.vus)
+                .concat(filteredAndAnnotatedReport.germline);
+
+            return Promise.resolve(data);
+        },
+    }));
+
+    public mutationCache = new MobxPromiseCache<
+        { entrezGeneId: number },
+        Mutation[]
+    >(q => ({
+        await: () => [
+            this.studyToMutationMolecularProfile,
+            this.studyToDataQueryFilter,
+        ],
+        invoke: async () => {
+            return _.flatten(
+                await Promise.all(
+                    Object.keys(
+                        this.studyToMutationMolecularProfile.result!
+                    ).map(studyId => {
+                        const molecularProfileId = this
+                            .studyToMutationMolecularProfile.result![studyId]
+                            .molecularProfileId;
+                        const dataQueryFilter = this.studyToDataQueryFilter
+                            .result![studyId];
+
+                        if (
+                            !dataQueryFilter ||
+                            (_.isEmpty(dataQueryFilter.sampleIds) &&
+                                !dataQueryFilter.sampleListId)
+                        ) {
+                            return Promise.resolve([]);
+                        }
+
+                        if (molecularProfileId) {
+                            return client.fetchMutationsInMolecularProfileUsingPOST(
+                                {
+                                    molecularProfileId,
+                                    mutationFilter: {
+                                        entrezGeneIds: [q.entrezGeneId],
+                                        ...dataQueryFilter,
+                                    } as MutationFilter,
+                                    projection:
+                                        REQUEST_ARG_ENUM.PROJECTION_DETAILED,
+                                }
+                            );
+                        } else {
+                            return Promise.resolve([]);
+                        }
+                    })
+                )
+            );
+        },
+    }));
+
+    readonly getMutationPutativeDriverInfo = remoteData({
+        await: () => {
+            const toAwait = [];
+            if (this.driverAnnotationSettings.oncoKb) {
+                toAwait.push(this.oncoKbMutationAnnotationForOncoprint);
+            }
+            if (this.driverAnnotationSettings.hotspots) {
+                toAwait.push(this.isHotspotForOncoprint);
+            }
+            return toAwait;
+        },
+        invoke: () => {
+            return Promise.resolve((mutation: Mutation): {
+                oncoKb: string;
+                hotspots: boolean;
+                customDriverBinary: boolean;
+                customDriverTier?: string;
+            } => {
+                const getOncoKbMutationAnnotationForOncoprint = this
+                    .oncoKbMutationAnnotationForOncoprint.result!;
+                const oncoKbDatum:
+                    | IndicatorQueryResp
+                    | undefined
+                    | null
+                    | false =
+                    this.driverAnnotationSettings.oncoKb &&
+                    getOncoKbMutationAnnotationForOncoprint &&
+                    !(
+                        getOncoKbMutationAnnotationForOncoprint instanceof Error
+                    ) &&
+                    getOncoKbMutationAnnotationForOncoprint(mutation);
+
+                const isHotspotDriver =
+                    this.driverAnnotationSettings.hotspots &&
+                    !(this.isHotspotForOncoprint.result instanceof Error) &&
+                    this.isHotspotForOncoprint.result!(mutation);
+
+                // Note: custom driver annotations are part of the incoming datum
+                return evaluatePutativeDriverInfoWithHotspots(
+                    mutation,
+                    oncoKbDatum,
+                    this.driverAnnotationSettings.customBinary,
+                    this.driverAnnotationSettings.driverTiers,
+                    {
+                        hotspotDriver: isHotspotDriver,
+                        hotspotAnnotationsActive: this.driverAnnotationSettings
+                            .hotspots,
+                    }
+                );
+            });
+        },
+        onError: () => {},
+    });
+
+    readonly oncoKbMutationAnnotationForOncoprint = remoteData<
+        Error | ((mutation: Mutation) => IndicatorQueryResp | undefined)
+    >({
+        await: () => [this.oncoKbDataForOncoprint],
+        invoke: () =>
+            makeGetOncoKbMutationAnnotationForOncoprint(
+                this.oncoKbDataForOncoprint
+            ),
+        onError: () => {},
+    });
+
+    //we need seperate oncokb data because oncoprint requires onkb queries across cancertype
+    //mutations tab the opposite
+    readonly oncoKbDataForOncoprint = remoteData<IOncoKbData | Error>(
+        {
+            await: () => [this.mutations, this.oncoKbAnnotatedGenes],
+            invoke: async () => {
+                return fetchOncoKbDataForOncoprint(
+                    this.oncoKbAnnotatedGenes,
+                    this.mutations
+                );
+            },
+            onError: (err: Error) => {
+                // fail silently, leave the error handling responsibility to the data consumer
+            },
+        },
+        ONCOKB_DEFAULT
+    );
+
+    readonly oncoKbAnnotatedGenes = remoteData(
+        {
+            await: () => [this.oncokbCancerGenes],
+            invoke: () => {
+                if (
+                    getServerConfig().show_oncokb &&
+                    !_.isError(this.oncokbCancerGenes.result)
+                ) {
+                    return Promise.resolve(
+                        _.reduce(
+                            this.oncokbCancerGenes.result,
+                            (
+                                map: { [entrezGeneId: number]: boolean },
+                                next: CancerGene
+                            ) => {
+                                if (next?.oncokbAnnotated) {
+                                    map[next.entrezGeneId] = true;
+                                }
+                                return map;
+                            },
+                            {}
+                        )
+                    );
+                } else {
+                    return Promise.resolve({});
+                }
+            },
+            onError: e => {},
+        },
+        {}
+    );
+
+    public readonly isHotspotForOncoprint = remoteData<
+        ((m: Mutation) => boolean) | Error
+    >({
+        invoke: () => makeIsHotspotForOncoprint(this.indexedHotspotData),
+        onError: () => {},
+    });
+
+    readonly indexedHotspotData = remoteData<IHotspotIndex | undefined>({
+        await: () => [this.hotspotData],
+        invoke: () => Promise.resolve(indexHotspotsData(this.hotspotData)),
+        onError: () => {},
+    });
+
+    // Hotspots
+    readonly hotspotData = remoteData({
+        await: () => [this.mutations],
+        invoke: () => {
+            return fetchHotspotsData(
+                this.mutations,
+                undefined,
+                this.genomeNexusInternalClient
+            );
+        },
+        onError: () => {},
+    });
+
+    @computed get genomeNexusInternalClient() {
+        const client = new GenomeNexusAPIInternal(this.referenceGenomeBuild);
+
+        client.addErrorHandler(err => {
+            eventBus.emit(
+                'error',
+                null,
+                new SiteError(
+                    new Error(ErrorMessages.GENOME_NEXUS_LOAD_ERROR),
+                    'alert'
+                )
+            );
+        });
+
+        return client;
+    }
+
+    @computed get referenceGenomeBuild() {
+        if (!this.displayedStudies.isComplete) {
+            throw new Error('Failed to get studies');
+        }
+        return getGenomeNexusUrl(this.displayedStudies.result);
+    }
 }
diff --git a/src/pages/studyView/StudyViewPageTabs.ts b/src/pages/studyView/StudyViewPageTabs.ts
index 0c8e4e2a26f..bc76f0292d6 100644
--- a/src/pages/studyView/StudyViewPageTabs.ts
+++ b/src/pages/studyView/StudyViewPageTabs.ts
@@ -4,6 +4,7 @@ export enum StudyViewPageTabKeyEnum {
     HEATMAPS = 'heatmaps',
     CN_SEGMENTS = 'cnSegments',
     FILES_AND_LINKS = 'filesAndLinks',
+    PLOTS = 'plots',
 }
 
 export const StudyViewResourceTabPrefix = 'openResource_';
diff --git a/src/pages/studyView/StudyViewURLWrapper.ts b/src/pages/studyView/StudyViewURLWrapper.ts
index 8ff2c745e04..5805e629554 100644
--- a/src/pages/studyView/StudyViewURLWrapper.ts
+++ b/src/pages/studyView/StudyViewURLWrapper.ts
@@ -6,13 +6,74 @@ import { PatientViewPageTabs } from '../patientView/PatientViewPageTabs';
 import { StudyViewPageTabKeyEnum } from './StudyViewPageTabs';
 import ExtendedRouterStore from '../../shared/lib/ExtendedRouterStore';
 
+export type PlotsSelectionParam = {
+    selectedGeneOption?: string;
+    selectedGenesetOption?: string;
+    selectedGenericAssayOption?: string;
+    dataType?: string;
+    selectedDataSourceOption?: string;
+    mutationCountBy?: string;
+    structuralVariantCountBy?: string;
+    logScale?: string;
+};
+
+const PlotsSelectionParamProps: Required<PlotsSelectionParam> = {
+    selectedGeneOption: '',
+    selectedGenesetOption: '',
+    selectedGenericAssayOption: '',
+    dataType: '',
+    selectedDataSourceOption: '',
+    mutationCountBy: '',
+    structuralVariantCountBy: '',
+    logScale: '',
+};
+
+export type PlotsColoringParam = {
+    selectedOption?: string;
+    logScale?: string;
+    colorByMutationType?: string;
+    colorByCopyNumber?: string;
+    colorBySv?: string;
+};
+
+const PlotsColoringParamProps: Required<PlotsColoringParam> = {
+    selectedOption: '',
+    logScale: '',
+    colorByMutationType: '',
+    colorByCopyNumber: '',
+    colorBySv: '',
+};
+
 export default class StudyViewURLWrapper extends URLWrapper<
-    Pick<StudyViewURLQuery, 'tab' | 'resourceUrl'>
+    Pick<
+        StudyViewURLQuery,
+        | 'tab'
+        | 'resourceUrl'
+        | 'plots_horz_selection'
+        | 'plots_vert_selection'
+        | 'plots_coloring_selection'
+        | 'geneset_list'
+        | 'generic_assay_groups'
+    >
 > {
     constructor(routing: ExtendedRouterStore) {
         super(routing, {
             tab: { isSessionProp: false },
             resourceUrl: { isSessionProp: false },
+            plots_horz_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsSelectionParamProps,
+            },
+            plots_vert_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsSelectionParamProps,
+            },
+            plots_coloring_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsColoringParamProps,
+            },
+            geneset_list: { isSessionProp: true },
+            generic_assay_groups: { isSessionProp: false },
         });
         makeObservable(this);
     }
diff --git a/src/routes.tsx b/src/routes.tsx
index 0f640d186da..5f508279c2e 100755
--- a/src/routes.tsx
+++ b/src/routes.tsx
@@ -110,7 +110,7 @@ import {
     PatientViewResourceTabPrefix,
 } from 'pages/patientView/PatientViewPageTabs';
 import { GroupComparisonTab } from 'pages/groupComparison/GroupComparisonTabs';
-import { CLIN_ATTR_DATA_TYPE } from 'pages/resultsView/plots/PlotsTabUtils';
+import { CLIN_ATTR_DATA_TYPE } from 'shared/components/plots/PlotsTabUtils';
 import { SpecialAttribute } from 'shared/cache/ClinicalDataCache';
 import { AlterationTypeConstants } from 'shared/constants';
 import {
diff --git a/src/shared/components/banners/AlterationFilterWarning.tsx b/src/shared/components/banners/AlterationFilterWarning.tsx
index 5fa6ec8862a..42cc9a950d0 100644
--- a/src/shared/components/banners/AlterationFilterWarning.tsx
+++ b/src/shared/components/banners/AlterationFilterWarning.tsx
@@ -1,12 +1,42 @@
 import * as React from 'react';
 import { observer } from 'mobx-react';
-import { ResultsViewPageStore } from '../../../pages/resultsView/ResultsViewPageStore';
 import { computed, makeObservable } from 'mobx';
 import { MakeMobxView } from '../MobxView';
 import classnames from 'classnames';
+import { DriverAnnotationSettings } from 'shared/alterationFiltering/AnnotationFilteringSettings';
+import { MobxPromise } from 'cbioportal-frontend-commons';
+import { FilteredAndAnnotatedMutationsReport } from 'shared/lib/comparison/AnalysisStoreUtils';
+import {
+    AnnotatedMutation,
+    AnnotatedStructuralVariant,
+} from 'shared/model/AnnotatedMutation';
+import { ExtendedAlteration } from 'shared/model/ExtendedAlteration';
+import { AnnotatedNumericGeneMolecularData } from 'shared/model/AnnotatedNumericGeneMolecularData';
 
 export interface IAlterationFilterWarningProps {
-    store: ResultsViewPageStore;
+    driverAnnotationSettings: DriverAnnotationSettings;
+    includeGermlineMutations: boolean;
+    mutationsReportByGene: MobxPromise<{
+        [hugeGeneSymbol: string]: FilteredAndAnnotatedMutationsReport<
+            AnnotatedMutation
+        >;
+    }>;
+    oqlFilteredMutationsReport: MobxPromise<{
+        data: (AnnotatedMutation & ExtendedAlteration)[];
+        vus: (AnnotatedMutation & ExtendedAlteration)[];
+        germline: (AnnotatedMutation & ExtendedAlteration)[];
+        vusAndGermline: (AnnotatedMutation & ExtendedAlteration)[];
+    }>;
+    oqlFilteredMolecularDataReport: MobxPromise<{
+        data: (AnnotatedNumericGeneMolecularData & ExtendedAlteration)[];
+        vus: (AnnotatedNumericGeneMolecularData & ExtendedAlteration)[];
+    }>;
+    oqlFilteredStructuralVariantsReport: MobxPromise<{
+        data: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        vus: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        germline: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        vusAndGermline: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+    }>;
     isUnaffected?: boolean;
     mutationsTabModeSettings?: {
         // if set, then we show in "mutations tab mode" - different text, different source of exclude state, and toggleable exclude state
@@ -48,7 +78,7 @@ export default class AlterationFilterWarning extends React.Component<
         if (this.props.mutationsTabModeSettings) {
             return this.props.mutationsTabModeSettings.excludeVUS;
         } else {
-            return !this.props.store.driverAnnotationSettings.includeVUS;
+            return !this.props.driverAnnotationSettings.includeVUS;
         }
     }
 
@@ -56,33 +86,33 @@ export default class AlterationFilterWarning extends React.Component<
         if (this.props.mutationsTabModeSettings) {
             return this.props.mutationsTabModeSettings.excludeGermline;
         } else {
-            return !this.props.store.includeGermlineMutations;
+            return !this.props.includeGermlineMutations;
         }
     }
 
     @computed get vusToggleable() {
         return (
             this.props.mutationsTabModeSettings &&
-            !this.props.store.driverAnnotationSettings.includeVUS
+            !this.props.driverAnnotationSettings.includeVUS
         );
     }
 
     @computed get germlineToggleable() {
         return (
             this.props.mutationsTabModeSettings &&
-            !this.props.store.includeGermlineMutations
+            !this.props.includeGermlineMutations
         );
     }
 
     readonly vusWarning = MakeMobxView({
         await: () => {
             if (this.props.mutationsTabModeSettings) {
-                return [this.props.store.mutationsReportByGene];
+                return [this.props.mutationsReportByGene];
             } else {
                 return [
-                    this.props.store.oqlFilteredMutationsReport,
-                    this.props.store.oqlFilteredMolecularDataReport,
-                    this.props.store.oqlFilteredStructuralVariantsReport,
+                    this.props.oqlFilteredMutationsReport,
+                    this.props.oqlFilteredMolecularDataReport,
+                    this.props.oqlFilteredStructuralVariantsReport,
                 ];
             }
         },
@@ -94,7 +124,7 @@ export default class AlterationFilterWarning extends React.Component<
                 structuralVariant: false,
             };
             if (this.props.mutationsTabModeSettings) {
-                const report = this.props.store.mutationsReportByGene.result![
+                const report = this.props.mutationsReportByGene.result![
                     this.props.mutationsTabModeSettings.hugoGeneSymbol
                 ];
                 vusCount = report.vus.length + report.vusAndGermline.length;
@@ -102,14 +132,14 @@ export default class AlterationFilterWarning extends React.Component<
                     vusTypes.mutation = true;
                 }
             } else {
-                const mutationReport = this.props.store
-                    .oqlFilteredMutationsReport.result!;
+                const mutationReport = this.props.oqlFilteredMutationsReport
+                    .result!;
                 const mutationVusCount =
                     mutationReport.vus.length +
                     mutationReport.vusAndGermline.length;
-                const cnaVusCount = this.props.store
-                    .oqlFilteredMolecularDataReport.result!.vus.length;
-                const structuralVariantVusCount = this.props.store
+                const cnaVusCount = this.props.oqlFilteredMolecularDataReport
+                    .result!.vus.length;
+                const structuralVariantVusCount = this.props
                     .oqlFilteredStructuralVariantsReport.result!.vus.length;
                 vusCount =
                     mutationVusCount + cnaVusCount + structuralVariantVusCount;
@@ -204,19 +234,19 @@ export default class AlterationFilterWarning extends React.Component<
     readonly germlineWarning = MakeMobxView({
         await: () => {
             if (this.props.mutationsTabModeSettings) {
-                return [this.props.store.mutationsReportByGene];
+                return [this.props.mutationsReportByGene];
             } else {
-                return [this.props.store.oqlFilteredMutationsReport];
+                return [this.props.oqlFilteredMutationsReport];
             }
         },
         render: () => {
             let report;
             if (this.props.mutationsTabModeSettings) {
-                report = this.props.store.mutationsReportByGene.result![
+                report = this.props.mutationsReportByGene.result![
                     this.props.mutationsTabModeSettings.hugoGeneSymbol
                 ];
             } else {
-                report = this.props.store.oqlFilteredMutationsReport.result!;
+                report = this.props.oqlFilteredMutationsReport.result!;
             }
 
             const germlineCount =
diff --git a/src/shared/components/banners/CaseFilterWarning.tsx b/src/shared/components/banners/CaseFilterWarning.tsx
index d0caf9d535e..cd64c343db4 100644
--- a/src/shared/components/banners/CaseFilterWarning.tsx
+++ b/src/shared/components/banners/CaseFilterWarning.tsx
@@ -1,11 +1,15 @@
 import * as React from 'react';
 import { observer } from 'mobx-react';
-import { ResultsViewPageStore } from '../../../pages/resultsView/ResultsViewPageStore';
 import { MakeMobxView } from '../MobxView';
-import { pluralize } from 'cbioportal-frontend-commons';
+import { MobxPromise, pluralize } from 'cbioportal-frontend-commons';
+import { Patient, Sample } from 'cbioportal-ts-api-client';
 
 export interface ICaseFilterWarningProps {
-    store: ResultsViewPageStore;
+    samples: MobxPromise<Sample[]>;
+    filteredSamples: MobxPromise<Sample[]>;
+    patients: MobxPromise<Patient[]>;
+    filteredPatients: MobxPromise<Patient[]>;
+    hideUnprofiledSamples: false | 'any' | 'totally';
     isPatientMode?: boolean;
     isUnaffected?: boolean;
 }
@@ -17,22 +21,22 @@ export default class CaseFilterWarning extends React.Component<
 > {
     readonly sampleWarning = MakeMobxView({
         await: () => [
-            this.props.store.samples,
-            this.props.store.filteredSamples,
-            this.props.store.patients,
-            this.props.store.filteredPatients,
+            this.props.samples,
+            this.props.filteredSamples,
+            this.props.patients,
+            this.props.filteredPatients,
         ],
         render: () => {
             let nFiltered: number;
             if (this.props.isPatientMode) {
-                const nPatients = this.props.store.patients.result!.length;
-                const nFilteredPatients = this.props.store.filteredPatients
-                    .result!.length;
+                const nPatients = this.props.patients.result!.length;
+                const nFilteredPatients = this.props.filteredPatients.result!
+                    .length;
                 nFiltered = nPatients - nFilteredPatients;
             } else {
-                const nSamples = this.props.store.samples.result!.length;
-                const nFilteredSamples = this.props.store.filteredSamples
-                    .result!.length;
+                const nSamples = this.props.samples.result!.length;
+                const nFilteredSamples = this.props.filteredSamples.result!
+                    .length;
                 nFiltered = nSamples - nFilteredSamples;
             }
             if (nFiltered === 0) {
@@ -43,7 +47,7 @@ export default class CaseFilterWarning extends React.Component<
             const it = nFiltered === 1 ? 'it' : 'they';
 
             let allOrAny;
-            switch (this.props.store.hideUnprofiledSamples) {
+            switch (this.props.hideUnprofiledSamples) {
                 // The language is confusing here... if `hideUnprofiledSamples` is `any`, that means that we
                 //  filter out samples if they are unprofiled in "any" genes or profiles. This corresponds to
                 //  filtering out samples that are not profiled for "all" queried genes and profiles. If `hideUnprofiledSamples`
diff --git a/src/shared/components/banners/OqlStatusBanner.tsx b/src/shared/components/banners/OqlStatusBanner.tsx
index b3528db4637..659ec67b236 100644
--- a/src/shared/components/banners/OqlStatusBanner.tsx
+++ b/src/shared/components/banners/OqlStatusBanner.tsx
@@ -1,12 +1,11 @@
 import * as React from 'react';
-import { ResultsViewPageStore } from '../../../pages/resultsView/ResultsViewPageStore';
 import { observer } from 'mobx-react';
 import classnames from 'classnames';
 import { computed, makeObservable } from 'mobx';
 import './styles.scss';
 
 interface IOqlStatusBannerProps {
-    store: ResultsViewPageStore;
+    queryContainsOql: boolean;
     tabReflectsOql: boolean;
     isUnaffected?: boolean;
     onToggle?: () => void;
@@ -44,7 +43,7 @@ export default class OqlStatusBanner extends React.Component<
     }
 
     render() {
-        if (this.props.store.queryContainsOql) {
+        if (this.props.queryContainsOql) {
             let className: string;
             let message: string;
             let iconClassName: string;
diff --git a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx
index fde9efce8e2..519a780dd2f 100644
--- a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx
+++ b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx
@@ -1954,12 +1954,37 @@ export default class ResultsViewOncoprint extends React.Component<
                 <div className={'tabMessageContainer'}>
                     <OqlStatusBanner
                         className="oncoprint-oql-status-banner"
-                        store={this.props.store}
+                        queryContainsOql={this.props.store.queryContainsOql}
                         tabReflectsOql={true}
                     />
-                    <AlterationFilterWarning store={this.props.store} />
+                    <AlterationFilterWarning
+                        driverAnnotationSettings={
+                            this.props.store.driverAnnotationSettings
+                        }
+                        includeGermlineMutations={
+                            this.props.store.includeGermlineMutations
+                        }
+                        mutationsReportByGene={
+                            this.props.store.mutationsReportByGene
+                        }
+                        oqlFilteredMutationsReport={
+                            this.props.store.oqlFilteredMutationsReport
+                        }
+                        oqlFilteredMolecularDataReport={
+                            this.props.store.oqlFilteredMolecularDataReport
+                        }
+                        oqlFilteredStructuralVariantsReport={
+                            this.props.store.oqlFilteredStructuralVariantsReport
+                        }
+                    />
                     <CaseFilterWarning
-                        store={this.props.store}
+                        samples={this.props.store.samples}
+                        filteredSamples={this.props.store.filteredSamples}
+                        patients={this.props.store.patients}
+                        filteredPatients={this.props.store.filteredPatients}
+                        hideUnprofiledSamples={
+                            this.props.store.hideUnprofiledSamples
+                        }
                         isPatientMode={
                             this.oncoprintAnalysisCaseType ===
                             OncoprintAnalysisCaseType.PATIENT
diff --git a/src/shared/components/plots/BoxScatterPlot.tsx b/src/shared/components/plots/BoxScatterPlot.tsx
index 19bd2f0a90e..0681bf22e1a 100644
--- a/src/shared/components/plots/BoxScatterPlot.tsx
+++ b/src/shared/components/plots/BoxScatterPlot.tsx
@@ -36,10 +36,7 @@ import {
 import autobind from 'autobind-decorator';
 import { dataPointIsLimited } from 'shared/components/plots/PlotUtils';
 import _ from 'lodash';
-import {
-    IAxisLogScaleParams,
-    IBoxScatterPlotPoint,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+import { IAxisLogScaleParams, IBoxScatterPlotPoint } from './PlotsTabUtils';
 import { Popover } from 'react-bootstrap';
 import * as ReactDOM from 'react-dom';
 import classnames from 'classnames';
diff --git a/src/pages/resultsView/plots/LastPlotsTabSelectionForDatatype.spec.ts b/src/shared/components/plots/LastPlotsTabSelectionForDatatype.spec.ts
similarity index 100%
rename from src/pages/resultsView/plots/LastPlotsTabSelectionForDatatype.spec.ts
rename to src/shared/components/plots/LastPlotsTabSelectionForDatatype.spec.ts
diff --git a/src/pages/resultsView/plots/LastPlotsTabSelectionForDatatype.ts b/src/shared/components/plots/LastPlotsTabSelectionForDatatype.ts
similarity index 100%
rename from src/pages/resultsView/plots/LastPlotsTabSelectionForDatatype.ts
rename to src/shared/components/plots/LastPlotsTabSelectionForDatatype.ts
diff --git a/src/shared/components/plots/MultipleCategoryBarPlotUtils.ts b/src/shared/components/plots/MultipleCategoryBarPlotUtils.ts
index 4364ebdf5d1..cd41f0325a0 100644
--- a/src/shared/components/plots/MultipleCategoryBarPlotUtils.ts
+++ b/src/shared/components/plots/MultipleCategoryBarPlotUtils.ts
@@ -1,4 +1,4 @@
-import { IStringAxisData } from '../../../pages/resultsView/plots/PlotsTabUtils';
+import { IStringAxisData } from './PlotsTabUtils';
 import _ from 'lodash';
 import { IMultipleCategoryBarPlotData } from '../../../pages/groupComparison/MultipleCategoryBarPlot';
 
diff --git a/src/shared/components/plots/MultipleCategoryHeatmap.tsx b/src/shared/components/plots/MultipleCategoryHeatmap.tsx
index 0095e975453..4538a5a59ee 100644
--- a/src/shared/components/plots/MultipleCategoryHeatmap.tsx
+++ b/src/shared/components/plots/MultipleCategoryHeatmap.tsx
@@ -9,7 +9,7 @@ import Oncoprint, {
 import autobind from 'autobind-decorator';
 import { InitParams, OncoprintJS } from 'oncoprintjs';
 import _ from 'lodash';
-import { IStringAxisData } from 'pages/resultsView/plots/PlotsTabUtils';
+import { IStringAxisData } from './PlotsTabUtils';
 
 export type IOncoprintHeatmapProps = {
     horzData?: IStringAxisData['data'];
diff --git a/src/shared/components/plots/PlotUtils.ts b/src/shared/components/plots/PlotUtils.ts
index ec1cf678de5..0ae516e97b9 100644
--- a/src/shared/components/plots/PlotUtils.ts
+++ b/src/shared/components/plots/PlotUtils.ts
@@ -1,10 +1,6 @@
 import _ from 'lodash';
 import jStat from 'jStat';
-import {
-    IPlotSampleData,
-    IThreshold1D,
-    IThreshold2D,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+import { IPlotSampleData, IThreshold1D, IThreshold2D } from './PlotsTabUtils';
 import {
     CBIOPORTAL_VICTORY_THEME,
     getTextHeight,
diff --git a/src/pages/resultsView/plots/PlotsTab.spec.tsx b/src/shared/components/plots/PlotsTab.spec.tsx
similarity index 95%
rename from src/pages/resultsView/plots/PlotsTab.spec.tsx
rename to src/shared/components/plots/PlotsTab.spec.tsx
index 7a61eff8cbd..7002ea7af5d 100644
--- a/src/pages/resultsView/plots/PlotsTab.spec.tsx
+++ b/src/shared/components/plots/PlotsTab.spec.tsx
@@ -1,5 +1,4 @@
 import { assert } from 'chai';
-import { AxisMenuSelection } from 'pages/resultsView/plots/PlotsTab';
 import { AlterationTypeConstants } from 'shared/constants';
 
 describe('PlotsTab', () => {
diff --git a/src/pages/resultsView/plots/PlotsTab.tsx b/src/shared/components/plots/PlotsTab.tsx
similarity index 82%
rename from src/pages/resultsView/plots/PlotsTab.tsx
rename to src/shared/components/plots/PlotsTab.tsx
index 79d4fcd4c64..814df5b16f7 100644
--- a/src/pages/resultsView/plots/PlotsTab.tsx
+++ b/src/shared/components/plots/PlotsTab.tsx
@@ -9,10 +9,10 @@ import {
 } from 'mobx';
 import { Observer, observer } from 'mobx-react';
 import './styles.scss';
-import { ResultsViewPageStore } from '../ResultsViewPageStore';
 import { AlterationTypeConstants, DataTypeConstants } from 'shared/constants';
 import { Button, FormControl } from 'react-bootstrap';
 import ReactSelect from 'react-select1';
+import AsyncSelect from 'react-select/async';
 import Select from 'react-select';
 import _ from 'lodash';
 import {
@@ -64,6 +64,8 @@ import {
     maybeSetLogScale,
     logScalePossibleForProfile,
     isGenericAssaySelected,
+    showWaterfallPlot,
+    getOption,
 } from './PlotsTabUtils';
 import {
     ClinicalAttribute,
@@ -72,6 +74,12 @@ import {
     ClinicalData,
     CancerStudy,
     MolecularProfile,
+    Sample,
+    Geneset,
+    StructuralVariant,
+    NumericGeneMolecularData,
+    GenePanelData,
+    Patient,
 } from 'cbioportal-ts-api-client';
 import ScatterPlot from 'shared/components/plots/ScatterPlot';
 import WaterfallPlot from 'shared/components/plots/WaterfallPlot';
@@ -81,40 +89,41 @@ import InfoIcon from '../../../shared/components/InfoIcon';
 import {
     CBIOPORTAL_VICTORY_THEME,
     DownloadControls,
+    MobxPromise,
+    MobxPromiseUnionType,
+    MobxPromiseUnionTypeWithDefault,
     remoteData,
     wrapText,
 } from 'cbioportal-frontend-commons';
-import { getRemoteDataGroupStatus } from 'cbioportal-utils';
+import { getRemoteDataGroupStatus, Mutation } from 'cbioportal-utils';
 import BoxScatterPlot, {
     IBoxScatterPlotData,
 } from '../../../shared/components/plots/BoxScatterPlot';
 import autobind from 'autobind-decorator';
 import fileDownload from 'react-file-download';
-import OqlStatusBanner from '../../../shared/components/banners/OqlStatusBanner';
 import {
     dataPointIsLimited,
     LegendDataWithId,
     scatterPlotSize,
 } from '../../../shared/components/plots/PlotUtils';
 import { getTablePlotDownloadData } from '../../../shared/components/plots/TablePlotUtils';
-import MultipleCategoryBarPlot from '../../groupComparison/MultipleCategoryBarPlot';
+import MultipleCategoryBarPlot from 'pages/groupComparison/MultipleCategoryBarPlot';
 import { RESERVED_CLINICAL_VALUE_COLORS } from 'shared/lib/Colors';
 import {
     DownloadControlOption,
-    MobxPromise,
     onMobxPromise,
 } from 'cbioportal-frontend-commons';
-import { showWaterfallPlot } from 'pages/resultsView/plots/PlotsTabUtils';
 import Pluralize from 'pluralize';
-import AlterationFilterWarning from '../../../shared/components/banners/AlterationFilterWarning';
 import LastPlotsTabSelectionForDatatype from './LastPlotsTabSelectionForDatatype';
 import { generateQuickPlots } from './QuickPlots';
 import ResultsViewURLWrapper, {
     PlotsSelectionParam,
-} from '../ResultsViewURLWrapper';
-import { SpecialAttribute } from '../../../shared/cache/ClinicalDataCache';
+    ResultsViewURLQuery,
+} from 'pages/resultsView/ResultsViewURLWrapper';
+import ClinicalDataCache, {
+    SpecialAttribute,
+} from '../../../shared/cache/ClinicalDataCache';
 import LabeledCheckbox from '../../../shared/components/labeledCheckbox/LabeledCheckbox';
-import CaseFilterWarning from '../../../shared/components/banners/CaseFilterWarning';
 import { getSuffixOfMolecularProfile } from 'shared/lib/molecularProfileUtils';
 import {
     COMMON_GENERIC_ASSAY_PROPERTY,
@@ -124,7 +133,7 @@ import {
     makeGenericAssayPlotsTabOption,
 } from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
 import { getBoxWidth } from 'shared/lib/boxPlotUtils';
-import ScrollWrapper from '../cancerSummary/ScrollWrapper';
+import ScrollWrapper from 'pages/resultsView/cancerSummary/ScrollWrapper';
 import {
     DEFAULT_GENERIC_ASSAY_OPTIONS_SHOWING,
     MenuList,
@@ -132,8 +141,32 @@ import {
 } from 'pages/studyView/addChartButton/genericAssaySelection/GenericAssaySelection';
 import { doesOptionMatchSearchText } from 'shared/lib/GenericAssayUtils/GenericAssaySelectionUtils';
 import { GENERIC_ASSAY_CONFIG } from 'shared/lib/GenericAssayUtils/GenericAssayConfig';
-import { allowExpressionCrossStudy } from 'shared/lib/allowExpressionCrossStudy';
 import { getServerConfig } from 'config/config';
+import { ExtendedClinicalAttribute } from 'pages/resultsView/ResultsViewPageStoreUtils';
+import MobxPromiseCache from 'shared/lib/MobxPromiseCache';
+import { CustomDriverNumericGeneMolecularData } from 'shared/model/CustomDriverNumericGeneMolecularData';
+import {
+    AnnotatedMutation,
+    AnnotatedStructuralVariant,
+} from 'shared/model/AnnotatedMutation';
+import {
+    CoverageInformation,
+    getCoverageInformation,
+} from 'shared/lib/GenePanelUtils';
+import GenesetMolecularDataCache from 'shared/cache/GenesetMolecularDataCache';
+import GenericAssayMolecularDataCache from 'shared/cache/GenericAssayMolecularDataCache';
+import { DriverAnnotationSettings } from 'shared/alterationFiltering/AnnotationFilteringSettings';
+import StudyViewURLWrapper from 'pages/studyView/StudyViewURLWrapper';
+import { StudyViewURLQuery } from 'pages/studyView/StudyViewPageStore';
+import { fetchGenes } from 'shared/lib/StoreUtils';
+import { Else, If, Then } from 'react-if';
+import { allowExpressionCrossStudy } from 'shared/lib/allowExpressionCrossStudy';
+import OqlStatusBanner from '../banners/OqlStatusBanner';
+import AlterationFilterWarning from '../banners/AlterationFilterWarning';
+import { FilteredAndAnnotatedMutationsReport } from 'shared/lib/comparison/AnalysisStoreUtils';
+import { AnnotatedNumericGeneMolecularData } from 'shared/model/AnnotatedNumericGeneMolecularData';
+import { ExtendedAlteration } from 'shared/model/ExtendedAlteration';
+import CaseFilterWarning from '../banners/CaseFilterWarning';
 
 enum EventKey {
     horz_logScale,
@@ -230,8 +263,109 @@ export type ColoringMenuSelection = {
 };
 
 export interface IPlotsTabProps {
-    store: ResultsViewPageStore;
-    urlWrapper: ResultsViewURLWrapper;
+    filteredSamplesByDetailedCancerType: MobxPromise<{
+        [cancerType: string]: Sample[];
+    }>;
+    mutations: MobxPromiseUnionType<Mutation[]>;
+    studies: MobxPromiseUnionTypeWithDefault<CancerStudy[]>;
+    molecularProfileIdSuffixToMolecularProfiles: MobxPromiseUnionTypeWithDefault<{
+        [molecularProfileIdSuffix: string]: MolecularProfile[];
+    }>;
+    entrezGeneIdToGene: MobxPromise<{
+        [entrezGeneId: number]: Gene;
+    }>;
+    sampleKeyToSample: MobxPromise<_.Dictionary<Sample>>;
+    genes: MobxPromise<Gene[]>;
+    clinicalAttributes: MobxPromise<ExtendedClinicalAttribute[]>;
+    genesets: MobxPromise<Geneset[]>;
+    genericAssayEntitiesGroupByMolecularProfileId: MobxPromise<{
+        [profileId: string]: GenericAssayMeta[];
+    }>;
+    studyIds: MobxPromise<string[]>;
+    molecularProfilesWithData: MobxPromise<MolecularProfile[]>;
+    molecularProfilesInStudies: MobxPromiseUnionTypeWithDefault<
+        MolecularProfile[]
+    >;
+    annotatedCnaCache: MobxPromiseCache<
+        {
+            entrezGeneId: number;
+        },
+        CustomDriverNumericGeneMolecularData[]
+    >;
+    annotatedMutationCache: MobxPromiseCache<
+        {
+            entrezGeneId: number;
+        },
+        AnnotatedMutation[]
+    >;
+    structuralVariantCache: MobxPromiseCache<
+        {
+            entrezGeneId: number;
+        },
+        StructuralVariant[]
+    >;
+    studyToMutationMolecularProfile: MobxPromise<{
+        [studyId: string]: MolecularProfile;
+    }>;
+    studyToMolecularProfileDiscreteCna: MobxPromise<{
+        [studyId: string]: MolecularProfile;
+    }>;
+    clinicalDataCache: ClinicalDataCache;
+    patientKeyToFilteredSamples: MobxPromise<_.Dictionary<Sample[]>>;
+    numericGeneMolecularDataCache: MobxPromiseCache<
+        {
+            entrezGeneId: number;
+            molecularProfileId: string;
+        },
+        NumericGeneMolecularData[]
+    >;
+    coverageInformation: MobxPromise<CoverageInformation>;
+    genesetMolecularDataCache: MobxPromise<GenesetMolecularDataCache>;
+    genericAssayMolecularDataCache: MobxPromise<GenericAssayMolecularDataCache>;
+    studyToStructuralVariantMolecularProfile: MobxPromise<{
+        [studyId: string]: MolecularProfile;
+    }>;
+    driverAnnotationSettings: DriverAnnotationSettings;
+    studyIdToStudy?: _.Dictionary<CancerStudy>;
+    structuralVariants?: StructuralVariant[];
+    hugoGeneSymbols: string[];
+    selectedGenericAssayEntitiesGroupByMolecularProfileId: {
+        [molecularProfileId: string]: string[];
+    };
+    molecularProfileIdToMolecularProfile: MobxPromiseUnionTypeWithDefault<{
+        [molecularProfileId: string]: MolecularProfile;
+    }>;
+    urlWrapper: ResultsViewURLWrapper | StudyViewURLWrapper;
+    hasNoQueriedGenes?: boolean;
+    genePanelDataForAllProfiles?: GenePanelData[];
+    queryContainsOql?: boolean;
+    includeGermlineMutations?: boolean;
+    mutationsReportByGene?: MobxPromise<{
+        [hugeGeneSymbol: string]: FilteredAndAnnotatedMutationsReport<
+            AnnotatedMutation
+        >;
+    }>;
+    oqlFilteredMutationsReport?: MobxPromise<{
+        data: (AnnotatedMutation & ExtendedAlteration)[];
+        vus: (AnnotatedMutation & ExtendedAlteration)[];
+        germline: (AnnotatedMutation & ExtendedAlteration)[];
+        vusAndGermline: (AnnotatedMutation & ExtendedAlteration)[];
+    }>;
+    oqlFilteredMolecularDataReport?: MobxPromise<{
+        data: (AnnotatedNumericGeneMolecularData & ExtendedAlteration)[];
+        vus: (AnnotatedNumericGeneMolecularData & ExtendedAlteration)[];
+    }>;
+    oqlFilteredStructuralVariantsReport?: MobxPromise<{
+        data: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        vus: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        germline: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+        vusAndGermline: (AnnotatedStructuralVariant & ExtendedAlteration)[];
+    }>;
+    samples?: MobxPromise<Sample[]>;
+    filteredSamples: MobxPromise<Sample[]>;
+    patients: MobxPromise<Patient[]>;
+    filteredPatients?: MobxPromise<Patient[]>;
+    hideUnprofiledSamples?: false | 'any' | 'totally';
 }
 
 export type PlotsTabDataSource = {
@@ -259,11 +393,11 @@ class PlotsTabWaterfallPlot extends WaterfallPlot<IWaterfallPlotData> {}
 const SVG_ID = 'plots-tab-plot-svg';
 
 export const NONE_SELECTED_OPTION_STRING_VALUE = 'none';
-export const NONE_SELECTED_OPTION_NUMERICAL_VALUE = -1;
+export const NONE_SELECTED_OPTION_NUMERICAL_VALUE = -10000;
 export const NONE_SELECTED_OPTION_LABEL = 'Ordered samples';
-export const ALL_SELECTED_OPTION_NUMERICAL_VALUE = -3;
+export const ALL_SELECTED_OPTION_NUMERICAL_VALUE = -30000;
 export const SAME_SELECTED_OPTION_STRING_VALUE = 'same';
-export const SAME_SELECTED_OPTION_NUMERICAL_VALUE = -2;
+export const SAME_SELECTED_OPTION_NUMERICAL_VALUE = -20000;
 const LEGEND_TO_BOTTOM_WIDTH_THRESHOLD = 550; // when plot is wider than this value, the legend moves from right to bottom of screen
 const DISCRETE_CATEGORY_LIMIT = 150; // when a discrete variable has more categories, the discrete plot will not be rendered.
 
@@ -431,16 +565,16 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         if (
             !this.dataTypeOptions.isComplete ||
             !this.dataTypeToDataSourceOptions.isComplete ||
-            !this.props.store.filteredSamplesByDetailedCancerType.isComplete ||
-            !this.props.store.mutations.isComplete
+            !this.props.filteredSamplesByDetailedCancerType.isComplete ||
+            !this.props.mutations.isComplete
         ) {
             return <LoadingIndicator isLoading={true} size={'small'} />;
         }
 
         const cancerTypes = Object.keys(
-            this.props.store.filteredSamplesByDetailedCancerType.result
+            this.props.filteredSamplesByDetailedCancerType
         );
-        const mutationCount = this.props.store.mutations.result.length;
+        const mutationCount = this.props.mutations.result.length;
         const horizontalSource = this.horzSelection.selectedDataSourceOption
             ? this.horzSelection.selectedDataSourceOption.value
             : undefined;
@@ -549,8 +683,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     const studyIds = attributes.map(
                         attribute => attribute.studyId
                     );
-                    horzAxisStudies = this.props.store.studies.result.filter(
-                        study => studyIds.includes(study.studyId)
+                    horzAxisStudies = this.props.studies.result.filter(study =>
+                        studyIds.includes(study.studyId)
                     );
                     components.push(
                         <div>
@@ -566,16 +700,16 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 // molecular profile
                 if (
                     this.horzSelection.dataSourceId !== undefined &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .isComplete
                 ) {
                     const studyIds = _.uniq(
-                        this.props.store.molecularProfileIdSuffixToMolecularProfiles.result[
+                        this.props.molecularProfileIdSuffixToMolecularProfiles.result[
                             this.horzSelection.dataSourceId
                         ].map(profile => profile.studyId)
                     );
-                    horzAxisStudies = this.props.store.studies.result.filter(
-                        study => studyIds.includes(study.studyId)
+                    horzAxisStudies = this.props.studies.result.filter(study =>
+                        studyIds.includes(study.studyId)
                     );
                     components.push(
                         <div>
@@ -609,8 +743,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     const studyIds = attributes.map(
                         attribute => attribute.studyId
                     );
-                    vertAxisStudies = this.props.store.studies.result.filter(
-                        study => studyIds.includes(study.studyId)
+                    vertAxisStudies = this.props.studies.result.filter(study =>
+                        studyIds.includes(study.studyId)
                     );
                     components.push(
                         <div>
@@ -626,16 +760,16 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 // molecular profile
                 if (
                     this.vertSelection.dataSourceId !== undefined &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .isComplete
                 ) {
                     const studyIds = _.uniq(
-                        this.props.store.molecularProfileIdSuffixToMolecularProfiles.result[
+                        this.props.molecularProfileIdSuffixToMolecularProfiles.result[
                             this.vertSelection.dataSourceId
                         ].map(profile => profile.studyId)
                     );
-                    vertAxisStudies = this.props.store.studies.result.filter(
-                        study => studyIds.includes(study.studyId)
+                    vertAxisStudies = this.props.studies.result.filter(study =>
+                        studyIds.includes(study.studyId)
                     );
                     components.push(
                         <div>
@@ -762,8 +896,15 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this._selectedGeneOption === undefined &&
                     geneOptions.length
                 ) {
-                    // select default if _selectedGeneOption is undefined and theres defaults to choose from
-                    return geneOptions[0];
+                    // if no queried genes, default is undefined, else default is first gene option
+                    if (self.props.hasNoQueriedGenes) {
+                        return undefined;
+                    } else {
+                        return getOption(
+                            geneOptions[0],
+                            self.isGeneProfiled(geneOptions[0].label)
+                        );
+                    }
                 } else if (
                     vertical &&
                     this._selectedGeneOption &&
@@ -777,9 +918,23 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 ) {
                     // if vertical gene option is "same as horizontal", and horizontal is clinical, then use the actual
                     //      gene option value instead of "Same gene" option value, because that would be slightly weird UX
-                    return self.horzSelection.selectedGeneOption;
+                    const selectedGeneOption =
+                        self.horzSelection.selectedGeneOption;
+                    if (selectedGeneOption) {
+                        return getOption(
+                            selectedGeneOption,
+                            self.isGeneProfiled(selectedGeneOption.label)
+                        );
+                    }
+                    return selectedGeneOption;
                 } else {
                     // otherwise, return stored value for this variable
+                    if (this._selectedGeneOption) {
+                        return getOption(
+                            this._selectedGeneOption,
+                            self.isGeneProfiled(this._selectedGeneOption.label)
+                        );
+                    }
                     return this._selectedGeneOption;
                 }
             },
@@ -808,6 +963,10 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     (this._dataType === undefined && dataTypeOptions.length) ||
                     selectedDataTypeDoesNotExist
                 ) {
+                    // if no queried genes, default is undefined
+                    if (self.props.hasNoQueriedGenes) {
+                        return undefined;
+                    }
                     // return computed default if _dataType is undefined and if there are options to select a default value from
                     if (
                         isAlterationTypePresent(
@@ -924,7 +1083,6 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 this._structuralVariantCountBy = s;
             },
             get logScale() {
-                //const horzAxisData = self.horzAxisDataPromise.result;
                 const axisData = vertical
                     ? self.vertAxisDataPromise.result
                     : self.horzAxisDataPromise.result;
@@ -1097,16 +1255,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 }
             },
             set _selectedGeneOption(o: any) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.selectedGeneOption =
-                            o && o.value;
-                    } else {
-                        currentParams.plots_horz_selection.selectedGeneOption =
-                            o && o.value;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.selectedGeneOption =
+                                o && o.value;
+                        } else {
+                            currentParams.plots_horz_selection!.selectedGeneOption =
+                                o && o.value;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _selectedGenesetOption() {
@@ -1129,16 +1291,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 }
             },
             set _selectedGenesetOption(o: any) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.selectedGenesetOption =
-                            o && o.value;
-                    } else {
-                        currentParams.plots_horz_selection.selectedGenesetOption =
-                            o && o.value;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.selectedGenesetOption =
+                                o && o.value;
+                        } else {
+                            currentParams.plots_horz_selection!.selectedGenesetOption =
+                                o && o.value;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _selectedGenericAssayOption() {
@@ -1161,16 +1327,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 }
             },
             set _selectedGenericAssayOption(o: any) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.selectedGenericAssayOption =
-                            o && o.value;
-                    } else {
-                        currentParams.plots_horz_selection.selectedGenericAssayOption =
-                            o && o.value;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.selectedGenericAssayOption =
+                                o && o.value;
+                        } else {
+                            currentParams.plots_horz_selection!.selectedGenericAssayOption =
+                                o && o.value;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _selectedDataSourceOption() {
@@ -1202,16 +1372,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 }
             },
             set _selectedDataSourceOption(o: any) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.selectedDataSourceOption =
-                            o && o.value;
-                    } else {
-                        currentParams.plots_horz_selection.selectedDataSourceOption =
-                            o && o.value;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.selectedDataSourceOption =
+                                o && o.value;
+                        } else {
+                            currentParams.plots_horz_selection!.selectedDataSourceOption =
+                                o && o.value;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _dataType() {
@@ -1223,18 +1397,22 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 return urlSelection.dataType;
             },
             set _dataType(d: string | undefined) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        (currentParams.plots_vert_selection as Partial<
-                            PlotsSelectionParam
-                        >).dataType = d;
-                    } else {
-                        (currentParams.plots_horz_selection as Partial<
-                            PlotsSelectionParam
-                        >).dataType = d;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            (currentParams.plots_vert_selection as Partial<
+                                PlotsSelectionParam
+                            >).dataType = d;
+                        } else {
+                            (currentParams.plots_horz_selection as Partial<
+                                PlotsSelectionParam
+                            >).dataType = d;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _mutationCountBy() {
@@ -1246,14 +1424,18 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 return urlSelection.mutationCountBy as MutationCountBy;
             },
             set _mutationCountBy(c: MutationCountBy) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.mutationCountBy = c;
-                    } else {
-                        currentParams.plots_horz_selection.mutationCountBy = c;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.mutationCountBy = c;
+                        } else {
+                            currentParams.plots_horz_selection!.mutationCountBy = c;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _structuralVariantCountBy() {
@@ -1265,14 +1447,18 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 return urlSelection.structuralVariantCountBy as StructuralVariantCountBy;
             },
             set _structuralVariantCountBy(c: StructuralVariantCountBy) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.structuralVariantCountBy = c;
-                    } else {
-                        currentParams.plots_horz_selection.structuralVariantCountBy = c;
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.structuralVariantCountBy = c;
+                        } else {
+                            currentParams.plots_horz_selection!.structuralVariantCountBy = c;
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
 
             get _logScale() {
@@ -1285,14 +1471,18 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 return ret;
             },
             set _logScale(l: boolean) {
-                self.props.urlWrapper.updateURL(currentParams => {
-                    if (vertical) {
-                        currentParams.plots_vert_selection.logScale = l.toString();
-                    } else {
-                        currentParams.plots_horz_selection.logScale = l.toString();
+                self.props.urlWrapper.updateURL(
+                    (
+                        currentParams: ResultsViewURLQuery | StudyViewURLQuery
+                    ) => {
+                        if (vertical) {
+                            currentParams.plots_vert_selection!.logScale = l.toString();
+                        } else {
+                            currentParams.plots_horz_selection!.logScale = l.toString();
+                        }
+                        return currentParams;
                     }
-                    return currentParams;
-                });
+                );
             },
             _genericAssayDataType: undefined,
             selectedCategories: [],
@@ -1334,13 +1524,43 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     });
 
                     if (!option) {
-                        // Otherwise, find first gene option
-                        option = options.find(
-                            o =>
-                                o.info.entrezGeneId !== undefined &&
-                                o.info.entrezGeneId !==
-                                    NONE_SELECTED_OPTION_NUMERICAL_VALUE
-                        );
+                        // if no queried genes, set color option to gene on the horz/vert axis if exists, else none
+                        if (self.props.hasNoQueriedGenes) {
+                            if (self.horzSelection.selectedGeneOption) {
+                                option = options.find(
+                                    o =>
+                                        o.info.entrezGeneId !== undefined &&
+                                        o.info.entrezGeneId !==
+                                            NONE_SELECTED_OPTION_NUMERICAL_VALUE &&
+                                        o.info.entrezGeneId ===
+                                            self.horzSelection
+                                                .selectedGeneOption!.value
+                                );
+                            } else if (self.vertSelection.selectedGeneOption) {
+                                option = options.find(
+                                    o =>
+                                        o.info.entrezGeneId !== undefined &&
+                                        o.info.entrezGeneId !==
+                                            NONE_SELECTED_OPTION_NUMERICAL_VALUE &&
+                                        o.info.entrezGeneId ===
+                                            self.vertSelection
+                                                .selectedGeneOption!.value
+                                );
+                            } else {
+                                option = options.find(
+                                    o =>
+                                        o.info.entrezGeneId ===
+                                        NONE_SELECTED_OPTION_NUMERICAL_VALUE
+                                );
+                            }
+                        } else {
+                            option = options.find(
+                                o =>
+                                    o.info.entrezGeneId !== undefined &&
+                                    o.info.entrezGeneId !==
+                                        NONE_SELECTED_OPTION_NUMERICAL_VALUE
+                            );
+                        }
                     }
                     return option;
                 } else {
@@ -1354,15 +1574,21 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 this._selectedOptionValue = o && o.value;
             },
             get _selectedOptionValue() {
-                return self.props.urlWrapper.query.plots_coloring_selection
+                return self.props.urlWrapper.query.plots_coloring_selection!
                     .selectedOption;
             },
             set _selectedOptionValue(v: string | undefined) {
                 runInAction(() => {
-                    self.props.urlWrapper.updateURL(currentQuery => {
-                        currentQuery.plots_coloring_selection.selectedOption = v;
-                        return currentQuery;
-                    });
+                    self.props.urlWrapper.updateURL(
+                        (
+                            currentQuery:
+                                | ResultsViewURLQuery
+                                | StudyViewURLQuery
+                        ) => {
+                            currentQuery.plots_coloring_selection!.selectedOption = v;
+                            return currentQuery;
+                        }
+                    );
                     // reset highlights
                     self.highlightedLegendItems.clear();
                 });
@@ -1370,20 +1596,22 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             get logScale() {
                 // default false
                 return (
-                    self.props.urlWrapper.query.plots_coloring_selection
+                    self.props.urlWrapper.query.plots_coloring_selection!
                         .logScale === 'true'
                 );
             },
             set logScale(s: boolean) {
-                self.props.urlWrapper.updateURL(currentQuery => {
-                    currentQuery.plots_coloring_selection.logScale = s.toString();
-                    return currentQuery;
-                });
+                self.props.urlWrapper.updateURL(
+                    (currentQuery: ResultsViewURLQuery | StudyViewURLQuery) => {
+                        currentQuery.plots_coloring_selection!.logScale = s.toString();
+                        return currentQuery;
+                    }
+                );
             },
             get colorByMutationType() {
                 // default true
                 return (
-                    self.props.urlWrapper.query.plots_coloring_selection
+                    self.props.urlWrapper.query.plots_coloring_selection!
                         .colorByMutationType !== 'false'
                 );
             },
@@ -1401,7 +1629,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             get colorByCopyNumberFromUrl() {
                 // default true
                 return (
-                    self.props.urlWrapper.query.plots_coloring_selection
+                    self.props.urlWrapper.query.plots_coloring_selection!
                         .colorByCopyNumber !== 'false'
                 );
             },
@@ -1420,7 +1648,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             get colorByStructuralVariantFromUrl() {
                 // default true
                 return (
-                    self.props.urlWrapper.query.plots_coloring_selection
+                    self.props.urlWrapper.query.plots_coloring_selection!
                         .colorBySv !== 'false'
                 );
             },
@@ -1432,28 +1660,34 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     @action
     setColorByMutationType(s: boolean) {
-        this.props.urlWrapper.updateURL(currentQuery => {
-            currentQuery.plots_coloring_selection.colorByMutationType = s.toString();
-            return currentQuery;
-        });
+        this.props.urlWrapper.updateURL(
+            (currentQuery: ResultsViewURLQuery | StudyViewURLQuery) => {
+                currentQuery.plots_coloring_selection!.colorByMutationType = s.toString();
+                return currentQuery;
+            }
+        );
         // reset highlights
         this.highlightedLegendItems.clear();
     }
     @action
     setColorByCopyNumber(s: boolean) {
-        this.props.urlWrapper.updateURL(currentQuery => {
-            currentQuery.plots_coloring_selection.colorByCopyNumber = s.toString();
-            return currentQuery;
-        });
+        this.props.urlWrapper.updateURL(
+            (currentQuery: ResultsViewURLQuery | StudyViewURLQuery) => {
+                currentQuery.plots_coloring_selection!.colorByCopyNumber = s.toString();
+                return currentQuery;
+            }
+        );
         // reset highlights
         this.highlightedLegendItems.clear();
     }
     @action
     setColorByStructuralVariant(s: boolean) {
-        this.props.urlWrapper.updateURL(currentQuery => {
-            currentQuery.plots_coloring_selection.colorBySv = s.toString();
-            return currentQuery;
-        });
+        this.props.urlWrapper.updateURL(
+            (currentQuery: ResultsViewURLQuery | StudyViewURLQuery) => {
+                currentQuery.plots_coloring_selection!.colorBySv = s.toString();
+                return currentQuery;
+            }
+        );
         // reset highlights
         this.highlightedLegendItems.clear();
     }
@@ -1492,8 +1726,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     private downloadData() {
         onMobxPromise<any>(
             [
-                this.props.store.entrezGeneIdToGene,
-                this.props.store.sampleKeyToSample,
+                this.props.entrezGeneIdToGene,
+                this.props.sampleKeyToSample,
                 this.horzLabel,
                 this.vertLabel,
             ],
@@ -1609,7 +1843,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     private getHorizontalAxisMenu() {
         if (
             !this.dataTypeOptions.isComplete ||
-            !this.dataTypeToDataSourceOptions.isComplete
+            !this.dataTypeToDataSourceOptions.isComplete ||
+            !this.props.coverageInformation.isComplete
         ) {
             return <span></span>;
         } else {
@@ -1624,7 +1859,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     private getVerticalAxisMenu() {
         if (
             !this.dataTypeOptions.isComplete ||
-            !this.dataTypeToDataSourceOptions.isComplete
+            !this.dataTypeToDataSourceOptions.isComplete ||
+            !this.props.coverageInformation.isComplete
         ) {
             return <span></span>;
         } else {
@@ -1771,14 +2007,27 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     });
 
     readonly horzGeneOptions = remoteData<{ value: number; label: string }[]>({
-        await: () => [this.props.store.genes],
+        await: () => [this.props.genes],
         invoke: () => {
-            return Promise.resolve(
-                this.props.store.genes.result!.map(gene => ({
-                    value: gene.entrezGeneId,
-                    label: gene.hugoGeneSymbol,
-                }))
-            );
+            if (this.props.hasNoQueriedGenes) {
+                return Promise.resolve(
+                    this.props.genes
+                        .result!.map(gene => ({
+                            value: gene.entrezGeneId,
+                            label: gene.hugoGeneSymbol,
+                        }))
+                        .sort((a, b) => {
+                            return a.label < b.label ? -1 : 1;
+                        })
+                );
+            } else {
+                return Promise.resolve(
+                    this.props.genes.result!.map(gene => ({
+                        value: gene.entrezGeneId,
+                        label: gene.hugoGeneSymbol,
+                    }))
+                );
+            }
         },
     });
 
@@ -1817,10 +2066,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     readonly coloringMenuOmnibarOptions = remoteData<
         (ColoringMenuOmnibarOption | ColoringMenuOmnibarGroup)[]
     >({
-        await: () => [
-            this.props.store.genes,
-            this.props.store.clinicalAttributes,
-        ],
+        await: () => [this.props.genes, this.props.clinicalAttributes],
         invoke: () => {
             const allOptions: (
                 | Omit<ColoringMenuOmnibarOption, 'value'>
@@ -1832,7 +2078,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             // add gene options
             allOptions.push({
                 label: 'Genes',
-                options: this.props.store.genes.result!.map(gene => ({
+                options: this.props.genes.result!.map(gene => ({
                     label: gene.hugoGeneSymbol,
                     info: {
                         entrezGeneId: gene.entrezGeneId,
@@ -1842,7 +2088,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
             allOptions.push({
                 label: 'Clinical Attributes',
-                options: this.props.store.clinicalAttributes
+                options: this.props.clinicalAttributes
                     .result!.filter(a => {
                         return (
                             a.clinicalAttributeId !==
@@ -1893,10 +2139,10 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     });
 
     readonly horzGenesetOptions = remoteData({
-        await: () => [this.props.store.genesets],
+        await: () => [this.props.genesets],
         invoke: () => {
             return Promise.resolve(
-                this.props.store.genesets.result!.map(geneset => ({
+                this.props.genesets.result!.map(geneset => ({
                     value: geneset.genesetId,
                     label: geneset.name,
                 }))
@@ -1939,13 +2185,10 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     readonly genericEntitiesGroupByEntityId = remoteData<{
         [entityId: string]: GenericAssayMeta;
     }>({
-        await: () => [
-            this.props.store.genericAssayEntitiesGroupByMolecularProfileId,
-        ],
+        await: () => [this.props.genericAssayEntitiesGroupByMolecularProfileId],
         invoke: () => {
             const result: { [entityId: string]: GenericAssayMeta } = _.chain(
-                this.props.store.genericAssayEntitiesGroupByMolecularProfileId
-                    .result
+                this.props.genericAssayEntitiesGroupByMolecularProfileId.result
             )
                 .values()
                 .flatten()
@@ -1958,35 +2201,33 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly horzGenericAssayOptions = remoteData({
         await: () => [
-            this.props.store.genericAssayEntitiesGroupByMolecularProfileId,
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.genericAssayEntitiesGroupByMolecularProfileId,
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
         ],
         invoke: () => {
             // different generic assay profile can holds different entities, use entites in selected profile
             if (
                 this.horzSelection.dataSourceId &&
-                this.props.store.molecularProfileIdSuffixToMolecularProfiles
-                    .result &&
-                this.props.store.molecularProfileIdSuffixToMolecularProfiles
-                    .result[this.horzSelection.dataSourceId]
+                this.props.molecularProfileIdSuffixToMolecularProfiles.result &&
+                this.props.molecularProfileIdSuffixToMolecularProfiles.result[
+                    this.horzSelection.dataSourceId
+                ]
             ) {
                 return Promise.resolve(
                     _.chain(
-                        this.props.store
-                            .molecularProfileIdSuffixToMolecularProfiles.result[
-                            this.horzSelection.dataSourceId!
-                        ]
+                        this.props.molecularProfileIdSuffixToMolecularProfiles
+                            .result[this.horzSelection.dataSourceId!]
                     )
                         .reduce((acc, profile) => {
                             if (
-                                this.props.store
+                                this.props
                                     .genericAssayEntitiesGroupByMolecularProfileId
                                     .result &&
-                                this.props.store
+                                this.props
                                     .genericAssayEntitiesGroupByMolecularProfileId
                                     .result[profile.molecularProfileId]
                             ) {
-                                this.props.store.genericAssayEntitiesGroupByMolecularProfileId.result[
+                                this.props.genericAssayEntitiesGroupByMolecularProfileId.result[
                                     profile.molecularProfileId
                                 ].forEach(meta => {
                                     acc[meta.stableId] = { meta, profile };
@@ -2011,8 +2252,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly vertGenericAssayOptions = remoteData({
         await: () => [
-            this.props.store.genericAssayEntitiesGroupByMolecularProfileId,
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.genericAssayEntitiesGroupByMolecularProfileId,
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
         ],
         invoke: () => {
             let sameGenericAssayOption = undefined;
@@ -2027,27 +2268,25 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 // different generic assay profile can hold different entities, use entites in selected profile
                 if (
                     this.vertSelection.dataSourceId &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result[this.vertSelection.dataSourceId]
                 ) {
                     verticalOptions = _.chain(
-                        this.props.store
-                            .molecularProfileIdSuffixToMolecularProfiles.result[
-                            this.vertSelection.dataSourceId!
-                        ]
+                        this.props.molecularProfileIdSuffixToMolecularProfiles
+                            .result[this.vertSelection.dataSourceId!]
                     )
                         .reduce((acc, profile) => {
                             if (
-                                this.props.store
+                                this.props
                                     .genericAssayEntitiesGroupByMolecularProfileId
                                     .result &&
-                                this.props.store
+                                this.props
                                     .genericAssayEntitiesGroupByMolecularProfileId
                                     .result[profile.molecularProfileId]
                             ) {
-                                this.props.store.genericAssayEntitiesGroupByMolecularProfileId.result[
+                                this.props.genericAssayEntitiesGroupByMolecularProfileId.result[
                                     profile.molecularProfileId
                                 ].forEach(meta => {
                                     acc[meta.stableId] = { meta, profile };
@@ -2078,12 +2317,12 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.horzSelection.selectedGenericAssayOption &&
                     this.horzSelection.selectedGenericAssayOption.value !==
                         NONE_SELECTED_OPTION_STRING_VALUE &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result &&
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result[this.horzSelection.dataSourceId]
                 ) {
-                    const firstProfile = this.props.store
+                    const firstProfile = this.props
                         .molecularProfileIdSuffixToMolecularProfiles.result[
                         this.horzSelection.dataSourceId!
                     ][0];
@@ -2169,15 +2408,12 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     readonly clinicalAttributeIdToClinicalAttribute = remoteData<{
         [clinicalAttributeId: string]: ClinicalAttribute;
     }>({
-        await: () => [
-            this.props.store.clinicalAttributes,
-            this.props.store.studyIds,
-        ],
+        await: () => [this.props.clinicalAttributes, this.props.studyIds],
         invoke: () => {
             let _map: {
                 [clinicalAttributeId: string]: ClinicalAttribute;
             } = _.keyBy(
-                this.props.store.clinicalAttributes.result,
+                this.props.clinicalAttributes.result,
                 c => c.clinicalAttributeId
             );
             return Promise.resolve(_map);
@@ -2187,11 +2423,11 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     readonly clinicalAttributesGroupByclinicalAttributeId = remoteData<{
         [clinicalAttributeId: string]: ClinicalAttribute[];
     }>({
-        await: () => [this.props.store.clinicalAttributes],
+        await: () => [this.props.clinicalAttributes],
         invoke: () => {
             return Promise.resolve(
                 _.groupBy(
-                    this.props.store.clinicalAttributes.result,
+                    this.props.clinicalAttributes.result,
                     c => c.clinicalAttributeId
                 )
             );
@@ -2199,23 +2435,24 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     });
 
     readonly clinicalAttributeOptions = remoteData({
-        await: () => [this.props.store.clinicalAttributes],
+        await: () => [this.props.clinicalAttributes],
         invoke: () =>
             Promise.resolve(
                 makeClinicalAttributeOptions(
-                    this.props.store.clinicalAttributes.result!
+                    this.props.clinicalAttributes.result!
                 )
             ),
     });
 
     readonly dataTypeOptions = remoteData<PlotsTabOption[]>({
         await: () => [
-            this.props.store.molecularProfilesWithData,
+            this.props.molecularProfilesWithData,
             this.clinicalAttributeOptions,
-            this.props.store.molecularProfilesInStudies,
+            this.props.molecularProfilesInStudies,
+            this.props.genesets,
         ],
         invoke: () => {
-            const profiles = this.props.store.molecularProfilesWithData.result!;
+            const profiles = this.props.molecularProfilesWithData.result!;
 
             // show only data types we have profiles for
             const dataTypeIds: string[] = _.uniq(
@@ -2226,7 +2463,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
             // if no gene sets are queried, remove gene set profile from dataTypeIds
             if (
-                this.props.store.genesets.result!.length === 0 &&
+                this.props.genesets.result!.length === 0 &&
                 dataTypeIds.includes(AlterationTypeConstants.GENESET_SCORE)
             ) {
                 _.remove(dataTypeIds, function(n) {
@@ -2240,12 +2477,12 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             }
 
             if (
-                this.props.store.molecularProfilesInStudies.result!.length &&
+                this.props.molecularProfilesInStudies.result!.length &&
                 this.horzGenesetOptions.result &&
                 this.horzGenesetOptions.result!.length > 0
             ) {
                 // add geneset profile to list if the study contains it and the query contains gene sets
-                this.props.store.molecularProfilesInStudies.result.filter(p => {
+                this.props.molecularProfilesInStudies.result.filter(p => {
                     if (
                         p.molecularAlterationType ===
                         AlterationTypeConstants[GENESET_DATA_TYPE]
@@ -2293,12 +2530,11 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         [dataType: string]: { value: string; label: string }[];
     }>({
         await: () => [
-            this.props.store.molecularProfilesInStudies,
+            this.props.molecularProfilesInStudies,
             this.clinicalAttributeOptions,
         ],
         invoke: () => {
-            const profiles = this.props.store.molecularProfilesInStudies
-                .result!;
+            const profiles = this.props.molecularProfilesInStudies.result!;
             // filter out generic assay profile which showProfileInAnalysisTab is not TRUE
             const filteredProfiles = _.filter(profiles, profile => {
                 return (
@@ -2465,18 +2701,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             )
                 ? this.horzSelection.selectedGeneOption
                 : this.vertSelection.selectedGeneOption;
-            this.updateColoringMenuGene(selectedGene!.value);
+            selectedGene && this.updateColoringMenuGene(selectedGene.value);
 
             // for two genes, if the current gene for coloring is not selected in either axis, switch to gene selection on x-axis
         } else if (
             this.bothAxesMolecularProfile &&
+            this.horzSelection.selectedGeneOption &&
             currentSelectedGeneId !==
-                this.horzSelection.selectedGeneOption!.value &&
+                this.horzSelection.selectedGeneOption.value &&
+            this.vertSelection.selectedGeneOption &&
             currentSelectedGeneId !==
-                this.vertSelection.selectedGeneOption!.value
+                this.vertSelection.selectedGeneOption.value
         ) {
             this.updateColoringMenuGene(
-                this.horzSelection.selectedGeneOption!.value
+                this.horzSelection.selectedGeneOption.value
             );
         }
 
@@ -2692,7 +2930,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly cnaPromiseForColoring = remoteData({
         await: () =>
-            this.props.store.annotatedCnaCache.getAll(
+            this.props.annotatedCnaCache.getAll(
                 getCacheQueries(this.coloringMenuSelection)
             ),
         invoke: () => {
@@ -2700,7 +2938,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             if (queries.length > 0) {
                 return Promise.resolve(
                     _.flatten(
-                        this.props.store.annotatedCnaCache
+                        this.props.annotatedCnaCache
                             .getAll(queries)
                             .map(p => p.result!)
                     )
@@ -2721,13 +2959,13 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly mutationPromiseForColoring = remoteData({
         await: () =>
-            this.props.store.annotatedMutationCache.getAll(
+            this.props.annotatedMutationCache.getAll(
                 getCacheQueries(this.coloringMenuSelection)
             ),
         invoke: () => {
             return Promise.resolve(
                 _.flatten(
-                    this.props.store.annotatedMutationCache
+                    this.props.annotatedMutationCache
                         .getAll(getCacheQueries(this.coloringMenuSelection))
                         .map(p => p.result!)
                 ).filter(x => !!x)
@@ -2737,13 +2975,13 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly structuralVariantPromise = remoteData({
         await: () =>
-            this.props.store.structuralVariantCache.getAll(
+            this.props.structuralVariantCache.getAll(
                 getCacheQueries(this.coloringMenuSelection)
             ),
         invoke: () => {
             return Promise.resolve(
                 _.flatten(
-                    this.props.store.structuralVariantCache
+                    this.props.structuralVariantCache
                         .getAll(getCacheQueries(this.coloringMenuSelection))
                         .map(p => p.result!)
                 ).filter(x => !!x)
@@ -2755,7 +2993,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         if (this.mutationDataExists.result) {
             return {
                 molecularProfileIds: _.values(
-                    this.props.store.studyToMutationMolecularProfile.result!
+                    this.props.studyToMutationMolecularProfile.result!
                 ).map(p => p.molecularProfileId),
                 data: this.mutationPromiseForColoring.result!,
             };
@@ -2768,7 +3006,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         if (this.cnaDataExists.result) {
             return {
                 molecularProfileIds: _.values(
-                    this.props.store.studyToMolecularProfileDiscreteCna.result!
+                    this.props.studyToMolecularProfileDiscreteCna.result!
                 ).map(p => p.molecularProfileId),
                 data: this.cnaPromiseForColoring.result!,
             };
@@ -2783,7 +3021,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             this.coloringMenuSelection.selectedOption &&
             this.coloringMenuSelection.selectedOption.info.clinicalAttribute
         ) {
-            const promise = this.props.store.clinicalDataCache.get(
+            const promise = this.props.clinicalDataCache.get(
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             );
             clinicalData = promise.result!.data as ClinicalData[];
@@ -2810,17 +3048,17 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         return makeAxisDataPromise(
             this.horzSelection,
             this.clinicalAttributeIdToClinicalAttribute,
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
-            this.props.store.patientKeyToFilteredSamples,
-            this.props.store.entrezGeneIdToGene,
-            this.props.store.clinicalDataCache,
-            this.props.store.annotatedMutationCache,
-            this.props.store.structuralVariantCache,
-            this.props.store.numericGeneMolecularDataCache,
-            this.props.store.coverageInformation,
-            this.props.store.filteredSamples,
-            this.props.store.genesetMolecularDataCache,
-            this.props.store.genericAssayMolecularDataCache
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.patientKeyToFilteredSamples,
+            this.props.entrezGeneIdToGene,
+            this.props.clinicalDataCache,
+            this.props.annotatedMutationCache,
+            this.props.structuralVariantCache,
+            this.props.numericGeneMolecularDataCache,
+            this.props.coverageInformation,
+            this.props.filteredSamples,
+            this.props.genesetMolecularDataCache,
+            this.props.genericAssayMolecularDataCache
         );
     }
 
@@ -2837,17 +3075,17 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         return makeAxisDataPromise(
             this.vertSelection,
             this.clinicalAttributeIdToClinicalAttribute,
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
-            this.props.store.patientKeyToFilteredSamples,
-            this.props.store.entrezGeneIdToGene,
-            this.props.store.clinicalDataCache,
-            this.props.store.annotatedMutationCache,
-            this.props.store.structuralVariantCache,
-            this.props.store.numericGeneMolecularDataCache,
-            this.props.store.coverageInformation,
-            this.props.store.filteredSamples,
-            this.props.store.genesetMolecularDataCache,
-            this.props.store.genericAssayMolecularDataCache
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.patientKeyToFilteredSamples,
+            this.props.entrezGeneIdToGene,
+            this.props.clinicalDataCache,
+            this.props.annotatedMutationCache,
+            this.props.structuralVariantCache,
+            this.props.numericGeneMolecularDataCache,
+            this.props.coverageInformation,
+            this.props.filteredSamples,
+            this.props.genesetMolecularDataCache,
+            this.props.genericAssayMolecularDataCache
         );
     }
 
@@ -2881,36 +3119,31 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     }
 
     readonly mutationDataExists = remoteData({
-        await: () => [this.props.store.studyToMutationMolecularProfile],
+        await: () => [this.props.studyToMutationMolecularProfile],
         invoke: () => {
             return Promise.resolve(
-                _.values(
-                    this.props.store.studyToMutationMolecularProfile.result
-                ).length > 0
+                _.values(this.props.studyToMutationMolecularProfile.result)
+                    .length > 0
             );
         },
     });
 
     readonly cnaDataExists = remoteData({
-        await: () => [this.props.store.studyToMolecularProfileDiscreteCna],
+        await: () => [this.props.studyToMolecularProfileDiscreteCna],
         invoke: () => {
             return Promise.resolve(
-                _.values(
-                    this.props.store.studyToMolecularProfileDiscreteCna.result
-                ).length > 0
+                _.values(this.props.studyToMolecularProfileDiscreteCna.result)
+                    .length > 0
             );
         },
     });
 
     readonly svDataExists = remoteData({
-        await: () => [
-            this.props.store.studyToStructuralVariantMolecularProfile,
-        ],
+        await: () => [this.props.studyToStructuralVariantMolecularProfile],
         invoke: () => {
             return Promise.resolve(
                 _.values(
-                    this.props.store.studyToStructuralVariantMolecularProfile
-                        .result
+                    this.props.studyToStructuralVariantMolecularProfile.result
                 ).length > 0
             );
         },
@@ -2918,8 +3151,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly horzLabel = remoteData({
         await: () => [
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
-            this.props.store.entrezGeneIdToGene,
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.entrezGeneIdToGene,
             this.clinicalAttributeIdToClinicalAttribute,
             this.plotType,
         ],
@@ -2927,9 +3160,9 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             return Promise.resolve(
                 getAxisLabel(
                     this.horzSelection,
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result!,
-                    this.props.store.entrezGeneIdToGene.result!,
+                    this.props.entrezGeneIdToGene.result!,
                     this.clinicalAttributeIdToClinicalAttribute.result!,
                     this.horzLogScaleFunction
                 )
@@ -2939,17 +3172,17 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly vertLabel = remoteData({
         await: () => [
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
-            this.props.store.entrezGeneIdToGene,
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.entrezGeneIdToGene,
             this.clinicalAttributeIdToClinicalAttribute,
         ],
         invoke: () => {
             return Promise.resolve(
                 getAxisLabel(
                     this.vertSelection,
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result!,
-                    this.props.store.entrezGeneIdToGene.result!,
+                    this.props.entrezGeneIdToGene.result!,
                     this.clinicalAttributeIdToClinicalAttribute.result!,
                     this.vertLogScaleFunction
                 )
@@ -2959,8 +3192,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
 
     readonly waterfallLabel = remoteData({
         await: () => [
-            this.props.store.molecularProfileIdSuffixToMolecularProfiles,
-            this.props.store.entrezGeneIdToGene,
+            this.props.molecularProfileIdSuffixToMolecularProfiles,
+            this.props.entrezGeneIdToGene,
             this.clinicalAttributeIdToClinicalAttribute,
             this.plotType,
         ],
@@ -2975,9 +3208,9 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             return Promise.resolve(
                 getAxisLabel(
                     selection,
-                    this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                    this.props.molecularProfileIdSuffixToMolecularProfiles
                         .result!,
-                    this.props.store.entrezGeneIdToGene.result!,
+                    this.props.entrezGeneIdToGene.result!,
                     this.clinicalAttributeIdToClinicalAttribute.result!,
                     logScaleFunc
                 )
@@ -3023,9 +3256,9 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             this.mutationDataExists.result!,
             this.cnaDataExists.result!,
             this.svDataExists.result!,
-            this.props.store.driverAnnotationSettings.driversAnnotated,
+            this.props.driverAnnotationSettings.driversAnnotated,
             this.coloringMenuSelection.selectedOption,
-            this.props.store.clinicalDataCache,
+            this.props.clinicalDataCache,
             this.coloringLogScale
         );
     }
@@ -3113,7 +3346,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     private scatterPlotTooltip(d: IScatterPlotData) {
         return scatterPlotTooltip(
             d,
-            this.props.store.studyIdToStudy.result! || {},
+            this.props.studyIdToStudy || {},
             this.horzLogScaleFunction,
             this.vertLogScaleFunction,
             this.coloringMenuSelection.selectedOption &&
@@ -3125,7 +3358,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     private waterfallPlotTooltip(d: IWaterfallPlotData) {
         return waterfallPlotTooltip(
             d,
-            this.props.store.studyIdToStudy.result || {},
+            this.props.studyIdToStudy || {},
             this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
         );
@@ -3137,7 +3370,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             if (this.boxPlotData.isComplete) {
                 content = boxPlotTooltip(
                     d,
-                    this.props.store.studyIdToStudy.result || {},
+                    this.props.studyIdToStudy || {},
                     this.boxPlotData.result.horizontal,
                     this.boxPlotData.result.horizontal
                         ? this.horzLogScaleFunction
@@ -3253,6 +3486,21 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         return !isValidMrnaProfile && hasNegativeNumbers;
     }
 
+    private isGeneProfiled(
+        gene: string,
+        coverageInformation?: CoverageInformation
+    ) {
+        const samples =
+            coverageInformation?.samples ||
+            this.props.coverageInformation.result?.samples;
+        if (samples) {
+            return Object.values(samples).some(
+                s => !_.isEmpty(s.allGenes) || !!s.byGene[gene]
+            );
+        }
+        return false;
+    }
+
     private getAxisMenu(
         vertical: boolean,
         dataSourceOptionsByType: {
@@ -3268,7 +3516,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             (axisSelection.dataType !== CLIN_ATTR_DATA_TYPE &&
                 axisSelection.dataType !==
                     AlterationTypeConstants.MUTATION_EXTENDED &&
-                !this.props.store.molecularProfileIdSuffixToMolecularProfiles
+                !this.props.molecularProfileIdSuffixToMolecularProfiles
                     .isComplete) ||
             (axisSelection.dataType &&
                 isGenericAssaySelected(axisSelection) &&
@@ -3304,7 +3552,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         // we don't want to allow the data to be viewed by variantClass (Variant Type in UI) so remove
         // that from the options
         const filterStructuralVariantOptions = _.every(
-            this.props.store.structuralVariants.result,
+            this.props.structuralVariants,
             sv => {
                 return !sv.variantClass || sv.variantClass === 'NA';
             }
@@ -3362,7 +3610,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     dataSourceValue
                 ].description;
             } else {
-                dataSourceDescription = this.props.store
+                dataSourceDescription = this.props
                     .molecularProfileIdSuffixToMolecularProfiles.result![
                     dataSourceValue
                 ][0].description;
@@ -3374,7 +3622,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             const otherDataSourceId = vertical
                 ? this.horzSelection.dataSourceId
                 : this.vertSelection.dataSourceId;
-            const otherProfileName = this.props.store
+            const otherProfileName = this.props
                 .molecularProfileIdSuffixToMolecularProfiles.result![
                 otherDataSourceId!
             ][0].name;
@@ -3431,7 +3679,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.vertGenericAssayOptions.result,
                     selectedEntities,
                     this._vertGenericAssaySearchText,
-                    this.props.store.hugoGeneSymbols,
+                    this.props.hugoGeneSymbols,
                     this.horzSelection.selectedGeneOption?.label,
                     GENERIC_ASSAY_CONFIG.genericAssayConfigByType[
                         axisSelection.dataType!
@@ -3459,7 +3707,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.horzGenericAssayOptions.result,
                     selectedEntities,
                     this._horzGenericAssaySearchText,
-                    this.props.store.hugoGeneSymbols,
+                    this.props.hugoGeneSymbols,
                     this.vertSelection.selectedGeneOption?.label,
                     GENERIC_ASSAY_CONFIG.genericAssayConfigByType[
                         axisSelection.dataType!
@@ -3487,6 +3735,49 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             ? this.vertAxisCategories
             : this.horzAxisCategories;
 
+        let optionsWithProfiledStatus, loadOptions;
+        if (this.props.hasNoQueriedGenes) {
+            loadOptions = async (inputText: string, callback: any) => {
+                if (!inputText) {
+                    callback([]);
+                }
+                const stringCompare = (item: any) =>
+                    item.label.startsWith(inputText.toUpperCase());
+                let options =
+                    (vertical
+                        ? this.vertGeneOptions.result
+                        : this.horzGeneOptions.result) || [];
+                options = options.filter(stringCompare).slice(0, 10);
+                const genes = await fetchGenes(options.map(o => o.label));
+                const coverageInformationPromise = getCoverageInformation(
+                    this.props.genePanelDataForAllProfiles!,
+                    this.props.sampleKeyToSample.result!,
+                    this.props.patients.result!,
+                    genes
+                );
+                const coverageInformation = await coverageInformationPromise.then(
+                    (coverageInformation: CoverageInformation) => {
+                        return coverageInformation;
+                    }
+                );
+                options = options.map(g =>
+                    getOption(
+                        g,
+                        this.isGeneProfiled(g.label, coverageInformation)
+                    )
+                );
+                callback(options);
+            };
+        } else {
+            let options =
+                (vertical
+                    ? this.vertGeneOptions.result
+                    : this.horzGeneOptions.result) || [];
+            optionsWithProfiledStatus = options.map(g =>
+                getOption(g, this.isGeneProfiled(g.label))
+            );
+        }
+
         return (
             <form className="main-form">
                 <h4 className="tab-title">
@@ -3654,41 +3945,83 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                 }}
                             >
                                 <label>Gene</label>
-                                <div style={{ display: 'flex' }}>
-                                    <ReactSelect
-                                        name={`${
-                                            vertical ? 'v' : 'h'
-                                        }-gene-selector`}
-                                        value={
-                                            axisSelection.selectedGeneOption
-                                                ? axisSelection
-                                                      .selectedGeneOption.value
-                                                : undefined
-                                        }
-                                        onChange={
-                                            vertical
-                                                ? this.onVerticalAxisGeneSelect
-                                                : this
-                                                      .onHorizontalAxisGeneSelect
-                                        }
-                                        isLoading={
-                                            this.horzGeneOptions.isPending
-                                        }
-                                        options={
-                                            (vertical
-                                                ? this.vertGeneOptions.result
-                                                : this.horzGeneOptions
-                                                      .result) || []
-                                        }
-                                        clearable={false}
-                                        searchable={false}
-                                        disabled={
-                                            axisSelection.dataType ===
-                                                CLIN_ATTR_DATA_TYPE ||
-                                            axisSelection.dataType ===
-                                                GENESET_DATA_TYPE
-                                        }
-                                    />
+                                <div className="Select">
+                                    <If
+                                        condition={this.props.hasNoQueriedGenes}
+                                    >
+                                        <Then>
+                                            <AsyncSelect
+                                                name={`${
+                                                    vertical ? 'v' : 'h'
+                                                }-gene-selector`}
+                                                value={
+                                                    axisSelection.selectedGeneOption
+                                                        ? axisSelection.selectedGeneOption
+                                                        : undefined
+                                                }
+                                                onChange={
+                                                    vertical
+                                                        ? this
+                                                              .onVerticalAxisGeneSelect
+                                                        : this
+                                                              .onHorizontalAxisGeneSelect
+                                                }
+                                                isLoading={
+                                                    this.horzGeneOptions
+                                                        .isPending
+                                                }
+                                                noOptionsMessage={() =>
+                                                    'Search for gene'
+                                                }
+                                                clearable={false}
+                                                searchable={false}
+                                                disabled={
+                                                    axisSelection.dataType ===
+                                                        CLIN_ATTR_DATA_TYPE ||
+                                                    axisSelection.dataType ===
+                                                        GENESET_DATA_TYPE
+                                                }
+                                                loadOptions={loadOptions}
+                                                cacheOptions={true}
+                                            />
+                                        </Then>
+                                        <Else>
+                                            <ReactSelect
+                                                name={`${
+                                                    vertical ? 'v' : 'h'
+                                                }-gene-selector`}
+                                                value={
+                                                    axisSelection.selectedGeneOption
+                                                        ? axisSelection
+                                                              .selectedGeneOption
+                                                              .value
+                                                        : undefined
+                                                }
+                                                onChange={
+                                                    vertical
+                                                        ? this
+                                                              .onVerticalAxisGeneSelect
+                                                        : this
+                                                              .onHorizontalAxisGeneSelect
+                                                }
+                                                isLoading={
+                                                    this.horzGeneOptions
+                                                        .isPending
+                                                }
+                                                options={
+                                                    optionsWithProfiledStatus
+                                                }
+                                                clearable={false}
+                                                searchable={false}
+                                                disabled={
+                                                    axisSelection.dataType ===
+                                                        CLIN_ATTR_DATA_TYPE ||
+                                                    axisSelection.dataType ===
+                                                        GENESET_DATA_TYPE
+                                                }
+                                            />
+                                        </Else>
+                                    </If>
                                 </div>
                             </div>
                         )}
@@ -3772,7 +4105,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                         isLoading={
                                             this.horzGenericAssayOptions
                                                 .isPending ||
-                                            this.props.store
+                                            this.props
                                                 .genericAssayEntitiesGroupByMolecularProfileId
                                                 .isPending
                                         }
@@ -3904,16 +4237,15 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
     @computed
     get selectedGenericAssayEntitiesGroupedByGenericAssayTypeFromUrl() {
         const result = _.reduce(
-            this.props.store
-                .selectedGenericAssayEntitiesGroupByMolecularProfileId,
+            this.props.selectedGenericAssayEntitiesGroupByMolecularProfileId,
             (acc, entityId, profileId) => {
                 if (
-                    this.props.store.molecularProfileIdToMolecularProfile
-                        .result[profileId]
+                    this.props.molecularProfileIdToMolecularProfile.result[
+                        profileId
+                    ]
                 ) {
-                    const type = this.props.store
-                        .molecularProfileIdToMolecularProfile.result[profileId]
-                        .genericAssayType;
+                    const type = this.props.molecularProfileIdToMolecularProfile
+                        .result[profileId].genericAssayType;
                     acc[type] = acc[type]
                         ? _.union(entityId, acc[type])
                         : entityId;
@@ -3955,10 +4287,12 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                       ])
                     : [];
             const queriedGeneRelatedOptions = isGeneRelatedOptions
-                ? filterGenericAssayOptionsByGenes(
-                      filteredOtherOptions,
-                      queriedHugoGeneSymbols
-                  )
+                ? this.props.hasNoQueriedGenes
+                    ? filteredOtherOptions
+                    : filterGenericAssayOptionsByGenes(
+                          filteredOtherOptions,
+                          queriedHugoGeneSymbols
+                      )
                 : [];
             filteredOtherOptions = [
                 ...selectedGeneRelatedOptions,
@@ -4273,7 +4607,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             if (entrezGeneId === undefined) {
                 entrezGeneId = NONE_SELECTED_OPTION_NUMERICAL_VALUE;
             }
-            return this.props.store.entrezGeneIdToGene.result![entrezGeneId];
+            return this.props.entrezGeneIdToGene.result![entrezGeneId];
         }
         return undefined;
     }
@@ -4304,24 +4638,24 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             const ret: MobxPromise<any>[] = [
                 this.horzAxisDataPromise,
                 this.vertAxisDataPromise,
-                this.props.store.sampleKeyToSample,
-                this.props.store.coverageInformation,
+                this.props.sampleKeyToSample,
+                this.props.coverageInformation,
                 this.mutationDataExists,
                 this.cnaDataExists,
                 this.structuralVariantPromise,
                 this.svDataExists,
-                this.props.store.studyToMutationMolecularProfile,
+                this.props.studyToMutationMolecularProfile,
                 this.mutationPromiseForColoring,
                 this.cnaPromiseForColoring,
-                this.props.store.studyToMolecularProfileDiscreteCna,
-                this.props.store.studyToStructuralVariantMolecularProfile,
+                this.props.studyToMolecularProfileDiscreteCna,
+                this.props.studyToStructuralVariantMolecularProfile,
             ];
             if (
                 this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             ) {
                 ret.push(
-                    this.props.store.clinicalDataCache.get(
+                    this.props.clinicalDataCache.get(
                         this.coloringMenuSelection.selectedOption.info
                             .clinicalAttribute
                     )
@@ -4335,7 +4669,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             ) {
-                const promise = this.props.store.clinicalDataCache.get(
+                const promise = this.props.clinicalDataCache.get(
                     this.coloringMenuSelection.selectedOption.info
                         .clinicalAttribute
                 );
@@ -4351,13 +4685,12 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                         makeScatterPlotData(
                             horzAxisData,
                             vertAxisData,
-                            this.props.store.sampleKeyToSample.result!,
-                            this.props.store.coverageInformation.result!
-                                .samples,
+                            this.props.sampleKeyToSample.result!,
+                            this.props.coverageInformation.result!.samples,
                             this.mutationDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToMutationMolecularProfile
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4368,7 +4701,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                             this.cnaDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToMolecularProfileDiscreteCna
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4378,7 +4711,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                             this.svDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToStructuralVariantMolecularProfile
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4402,23 +4735,23 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             const ret: MobxPromise<any>[] = [
                 this.horzAxisDataPromise,
                 this.vertAxisDataPromise,
-                this.props.store.sampleKeyToSample,
-                this.props.store.coverageInformation,
+                this.props.sampleKeyToSample,
+                this.props.coverageInformation,
                 this.mutationDataExists,
                 this.cnaDataExists,
                 this.structuralVariantPromise,
                 this.svDataExists,
-                this.props.store.studyToMutationMolecularProfile,
+                this.props.studyToMutationMolecularProfile,
                 this.mutationPromiseForColoring,
                 this.cnaPromiseForColoring,
-                this.props.store.studyToMolecularProfileDiscreteCna,
+                this.props.studyToMolecularProfileDiscreteCna,
             ];
             if (
                 this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             ) {
                 ret.push(
-                    this.props.store.clinicalDataCache.get(
+                    this.props.clinicalDataCache.get(
                         this.coloringMenuSelection.selectedOption.info
                             .clinicalAttribute
                     )
@@ -4432,7 +4765,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             ) {
-                const promise = this.props.store.clinicalDataCache.get(
+                const promise = this.props.clinicalDataCache.get(
                     this.coloringMenuSelection.selectedOption.info
                         .clinicalAttribute
                 );
@@ -4459,21 +4792,20 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                           .entrezGeneId
                     : null;
                 const selectedGene = entrezGeneId
-                    ? this.props.store.entrezGeneIdToGene.result![entrezGeneId]
+                    ? this.props.entrezGeneIdToGene.result![entrezGeneId]
                     : null;
 
                 if (isNumberData(axisData!)) {
                     return Promise.resolve({
                         data: makeWaterfallPlotData(
                             axisData as INumberAxisData,
-                            this.props.store.sampleKeyToSample.result!,
-                            this.props.store.coverageInformation.result!
-                                .samples,
+                            this.props.sampleKeyToSample.result!,
+                            this.props.coverageInformation.result!.samples,
                             selectedGene,
                             this.mutationDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToMutationMolecularProfile
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4484,7 +4816,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                             this.cnaDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToMolecularProfileDiscreteCna
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4494,7 +4826,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                             this.svDataExists.result
                                 ? {
                                       molecularProfileIds: _.values(
-                                          this.props.store
+                                          this.props
                                               .studyToStructuralVariantMolecularProfile
                                               .result!
                                       ).map(p => p.molecularProfileId),
@@ -4520,10 +4852,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         const dataSourceId: string | undefined = this.isHorizontalWaterfallPlot
             ? this.horzSelection.dataSourceId!
             : this.vertSelection.dataSourceId!;
-        const profile = this.props.store
-            .molecularProfileIdSuffixToMolecularProfiles.result![
-            dataSourceId
-        ][0];
+        const profile = this.props.molecularProfileIdSuffixToMolecularProfiles
+            .result![dataSourceId][0];
         return profile.pivotThreshold;
     }
 
@@ -4535,7 +4865,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             const dataSourceId =
                 this.horzSelection.dataSourceId ||
                 this.vertSelection.dataSourceId;
-            return this.props.store.molecularProfileIdSuffixToMolecularProfiles
+            return this.props.molecularProfileIdSuffixToMolecularProfiles
                 .result![dataSourceId!][0].sortOrder;
         }
         return this._waterfallPlotSortOrder!;
@@ -4578,23 +4908,23 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             const ret: MobxPromise<any>[] = [
                 this.horzAxisDataPromise,
                 this.vertAxisDataPromise,
-                this.props.store.sampleKeyToSample,
-                this.props.store.coverageInformation,
+                this.props.sampleKeyToSample,
+                this.props.coverageInformation,
                 this.mutationDataExists,
                 this.cnaDataExists,
                 this.structuralVariantPromise,
                 this.svDataExists,
-                this.props.store.studyToMutationMolecularProfile,
+                this.props.studyToMutationMolecularProfile,
                 this.mutationPromiseForColoring,
                 this.cnaPromiseForColoring,
-                this.props.store.studyToMolecularProfileDiscreteCna,
+                this.props.studyToMolecularProfileDiscreteCna,
             ];
             if (
                 this.coloringMenuSelection.selectedOption &&
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             ) {
                 ret.push(
-                    this.props.store.clinicalDataCache.get(
+                    this.props.clinicalDataCache.get(
                         this.coloringMenuSelection.selectedOption.info
                             .clinicalAttribute
                     )
@@ -4641,7 +4971,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.coloringMenuSelection.selectedOption.info
                         .clinicalAttribute
                 ) {
-                    const promise = this.props.store.clinicalDataCache.get(
+                    const promise = this.props.clinicalDataCache.get(
                         this.coloringMenuSelection.selectedOption.info
                             .clinicalAttribute
                     );
@@ -4651,13 +4981,13 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                 let data = makeBoxScatterPlotData(
                     categoryData,
                     numberData,
-                    this.props.store.sampleKeyToSample.result!,
-                    this.props.store.coverageInformation.result!.samples,
+                    this.props.sampleKeyToSample.result!,
+                    this.props.coverageInformation.result!.samples,
                     this.mutationDataExists.result
                         ? {
                               molecularProfileIds: _.values(
-                                  this.props.store
-                                      .studyToMutationMolecularProfile.result!
+                                  this.props.studyToMutationMolecularProfile
+                                      .result!
                               ).map(p => p.molecularProfileId),
                               data: this.mutationPromiseForColoring.result!,
                           }
@@ -4665,8 +4995,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.cnaDataExists.result
                         ? {
                               molecularProfileIds: _.values(
-                                  this.props.store
-                                      .studyToMolecularProfileDiscreteCna
+                                  this.props.studyToMolecularProfileDiscreteCna
                                       .result!
                               ).map(p => p.molecularProfileId),
                               data: this.cnaPromiseForColoring.result!,
@@ -4675,7 +5004,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     this.svDataExists.result
                         ? {
                               molecularProfileIds: _.values(
-                                  this.props.store
+                                  this.props
                                       .studyToStructuralVariantMolecularProfile
                                       .result!
                               ).map(p => p.molecularProfileId),
@@ -4761,6 +5090,33 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         );
     }
 
+    @computed get shouldShowNoDataTypesSelectedWarning() {
+        return (
+            this.dataTypeOptions.isComplete &&
+            this.dataTypeToDataSourceOptions.isComplete &&
+            (!this.horzSelection.dataType || !this.vertSelection.dataType)
+        );
+    }
+
+    @computed get shouldShowNoGenesSelectedWarning() {
+        return (
+            this.dataTypeOptions.isComplete &&
+            this.dataTypeToDataSourceOptions.isComplete &&
+            ((this.horzSelection.dataType &&
+                this.showGeneSelectBox(
+                    this.horzSelection.dataType,
+                    isGenericAssaySelected(this.horzSelection)
+                ) &&
+                !this.horzSelection.selectedGeneOption) ||
+                (this.vertSelection.dataType &&
+                    this.showGeneSelectBox(
+                        this.vertSelection.dataType,
+                        isGenericAssaySelected(this.vertSelection)
+                    ) &&
+                    !this.vertSelection.selectedGeneOption))
+        );
+    }
+
     @computed get showUtilitiesMenu() {
         return (
             this.plotType.isComplete &&
@@ -4782,7 +5138,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             this.coloringMenuSelection.selectedOption &&
             this.coloringMenuSelection.selectedOption.info.clinicalAttribute
         ) {
-            return this.props.store.clinicalDataCache.get(
+            return this.props.clinicalDataCache.get(
                 this.coloringMenuSelection.selectedOption.info.clinicalAttribute
             );
         } else {
@@ -4847,7 +5203,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             this.vertLabel,
             this.genericEntitiesGroupByEntityId,
             this.horzGenericAssayOptions,
-            this.props.store.studies,
+            this.props.studies,
         ];
         if (this.coloringClinicalDataPromise) {
             promises.push(this.coloringClinicalDataPromise);
@@ -4875,6 +5231,64 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
             );
         }
 
+        if (this.shouldShowNoDataTypesSelectedWarning) {
+            return (
+                <div className={'alert alert-info'}>
+                    Please select datatype(s).
+                </div>
+            );
+        }
+        if (this.shouldShowNoGenesSelectedWarning) {
+            return (
+                <div className={'alert alert-info'}>Please select gene(s).</div>
+            );
+        }
+
+        // options for coloring ***
+        const defaultOptions = this.coloringMenuOmnibarOptions.result
+            ? this.coloringMenuOmnibarOptions.result.map(o => {
+                  if ((o as any).label === 'Genes') {
+                      let filteredOption = Object.assign(
+                          {},
+                          o as ColoringMenuOmnibarGroup
+                      );
+                      filteredOption.options = (o as ColoringMenuOmnibarGroup).options.slice(
+                          0,
+                          20
+                      );
+                      return filteredOption;
+                  }
+                  return o;
+              })
+            : [];
+
+        const loadColoringOptions = (inputText: string, callback: any) => {
+            if (!inputText) {
+                callback([]);
+            }
+            const stringCompare = (item: any) =>
+                item.label.toUpperCase().includes(inputText.toUpperCase());
+            const noneCheck = (item: any) =>
+                item.label !== 'None' ||
+                item.label.toUpperCase().includes(inputText.toUpperCase());
+            const options = this.coloringMenuOmnibarOptions.result
+                ? this.coloringMenuOmnibarOptions.result.map(o => {
+                      if ((o as any).options) {
+                          let filteredOption = Object.assign(
+                              {},
+                              o as ColoringMenuOmnibarGroup
+                          );
+                          filteredOption.options = (o as ColoringMenuOmnibarGroup).options
+                              .filter(stringCompare)
+                              .slice(0, 20);
+                          return filteredOption;
+                      }
+                      return o;
+                  })
+                : [];
+            callback(options.filter(noneCheck));
+        };
+
         switch (groupStatus) {
             case 'pending':
                 return (
@@ -5025,8 +5439,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                         this.scatterPlotData.result,
                                         this.coloringTypes,
                                         PlotType.ScatterPlot,
-                                        this.props.store
-                                            .driverAnnotationSettings
+                                        this.props.driverAnnotationSettings
                                             .driversAnnotated,
                                         this.limitValueTypes,
                                         this.highlightedLegendItems,
@@ -5095,8 +5508,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                         this.waterfallPlotData.result.data,
                                         this.coloringTypes,
                                         PlotType.WaterfallPlot,
-                                        this.props.store
-                                            .driverAnnotationSettings
+                                        this.props.driverAnnotationSettings
                                             .driversAnnotated,
                                         this.limitValueTypes,
                                         this.highlightedLegendItems,
@@ -5167,8 +5579,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                         ),
                                         this.coloringTypes,
                                         PlotType.BoxPlot,
-                                        this.props.store
-                                            .driverAnnotationSettings
+                                        this.props.driverAnnotationSettings
                                             .driversAnnotated,
                                         this.limitValueTypes,
                                         this.highlightedLegendItems,
@@ -5244,37 +5655,83 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                             className="gene-select-background"
                                         >
                                             <div className="checkbox gene-select-container">
-                                                <Select
-                                                    className={
-                                                        'color-samples-toolbar-elt gene-select'
-                                                    }
-                                                    name={`utilities_geneSelectionBox`}
-                                                    value={
-                                                        this
-                                                            .coloringMenuSelection
-                                                            .selectedOption
-                                                    }
-                                                    onChange={
-                                                        this
-                                                            .onColoringMenuOptionSelect
-                                                    }
-                                                    isLoading={
-                                                        this.horzGeneOptions
-                                                            .isPending
-                                                    }
-                                                    options={
-                                                        this
-                                                            .coloringMenuOmnibarOptions
-                                                            .result
-                                                    }
-                                                    clearable={false}
-                                                    searchable={true}
-                                                    disabled={
-                                                        !this
-                                                            .coloringMenuOmnibarOptions
-                                                            .isComplete
+                                                <If
+                                                    condition={
+                                                        this.props
+                                                            .hasNoQueriedGenes
                                                     }
-                                                />
+                                                >
+                                                    <Then>
+                                                        <AsyncSelect
+                                                            className={
+                                                                'color-samples-toolbar-elt gene-select'
+                                                            }
+                                                            name={`utilities_geneSelectionBox`}
+                                                            value={
+                                                                this
+                                                                    .coloringMenuSelection
+                                                                    .selectedOption
+                                                            }
+                                                            onChange={
+                                                                this
+                                                                    .onColoringMenuOptionSelect
+                                                            }
+                                                            isLoading={
+                                                                this
+                                                                    .horzGeneOptions
+                                                                    .isPending
+                                                            }
+                                                            noOptionsMessage={() =>
+                                                                'Search for gene or clinical attribute'
+                                                            }
+                                                            clearable={false}
+                                                            searchable={true}
+                                                            disabled={
+                                                                !this
+                                                                    .coloringMenuOmnibarOptions
+                                                                    .isComplete
+                                                            }
+                                                            loadOptions={
+                                                                loadColoringOptions
+                                                            }
+                                                            cacheOptions={true}
+                                                        />
+                                                    </Then>
+                                                    <Else>
+                                                        <Select
+                                                            className={
+                                                                'color-samples-toolbar-elt gene-select'
+                                                            }
+                                                            name={`utilities_geneSelectionBox`}
+                                                            value={
+                                                                this
+                                                                    .coloringMenuSelection
+                                                                    .selectedOption
+                                                            }
+                                                            onChange={
+                                                                this
+                                                                    .onColoringMenuOptionSelect
+                                                            }
+                                                            isLoading={
+                                                                this
+                                                                    .horzGeneOptions
+                                                                    .isPending
+                                                            }
+                                                            options={
+                                                                this
+                                                                    .coloringMenuOmnibarOptions
+                                                                    .result
+                                                            }
+                                                            clearable={false}
+                                                            searchable={true}
+                                                            disabled={
+                                                                !this
+                                                                    .coloringMenuOmnibarOptions
+                                                                    .isComplete
+                                                            }
+                                                        />
+                                                    </Else>
+                                                </If>
                                             </div>
                                         </div>
                                         {this.coloringLogScalePossible && (
@@ -5435,7 +5892,6 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                                                                       .downloadData,
                                                                   disabled: !this
                                                                       .props
-                                                                      .store
                                                                       .entrezGeneIdToGene
                                                                       .isComplete,
                                                               },
@@ -5541,11 +5997,13 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
         return (
             <div data-test="PlotsTabEntireDiv">
                 <div className={'tabMessageContainer'}>
-                    <OqlStatusBanner
-                        className="plots-oql-status-banner"
-                        store={this.props.store}
-                        tabReflectsOql={false}
-                    />
+                    {!this.props.hasNoQueriedGenes && (
+                        <OqlStatusBanner
+                            className="plots-oql-status-banner"
+                            queryContainsOql={!!this.props.queryContainsOql}
+                            tabReflectsOql={false}
+                        />
+                    )}
 
                     {// we have always allowed expression data to be compared
                     // across study in the plots tab
@@ -5554,7 +6012,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     // that all studies must be pan_can
                     // so default to true
                     !allowExpressionCrossStudy(
-                        this.props.store.studies.result,
+                        this.props.studies.result,
                         getServerConfig().enable_cross_study_expression,
                         false
                     ) && (
@@ -5564,11 +6022,41 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                         </div>
                     )}
 
-                    <AlterationFilterWarning
-                        store={this.props.store}
-                        isUnaffected={true}
-                    />
-                    <CaseFilterWarning store={this.props.store} />
+                    {!this.props.hasNoQueriedGenes && (
+                        <>
+                            <AlterationFilterWarning
+                                driverAnnotationSettings={
+                                    this.props.driverAnnotationSettings
+                                }
+                                includeGermlineMutations={
+                                    !!this.props.includeGermlineMutations
+                                }
+                                mutationsReportByGene={
+                                    this.props.mutationsReportByGene!
+                                }
+                                oqlFilteredMutationsReport={
+                                    this.props.oqlFilteredMutationsReport!
+                                }
+                                oqlFilteredMolecularDataReport={
+                                    this.props.oqlFilteredMolecularDataReport!
+                                }
+                                oqlFilteredStructuralVariantsReport={
+                                    this.props
+                                        .oqlFilteredStructuralVariantsReport!
+                                }
+                                isUnaffected={true}
+                            />
+                            <CaseFilterWarning
+                                samples={this.props.samples!}
+                                filteredSamples={this.props.filteredSamples!}
+                                patients={this.props.patients!}
+                                filteredPatients={this.props.filteredPatients!}
+                                hideUnprofiledSamples={
+                                    this.props.hideUnprofiledSamples!
+                                }
+                            />
+                        </>
+                    )}
                 </div>
                 <div className={'plotsTab'}>
                     <div className="quickPlotsContainer">
@@ -5578,7 +6066,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps, {}> {
                     <div style={{ display: 'flex' }}>
                         <div className="leftColumn">
                             {this.dataTypeOptions.isComplete &&
-                            this.dataTypeToDataSourceOptions.isComplete ? (
+                            this.dataTypeToDataSourceOptions.isComplete &&
+                            this.props.coverageInformation.isComplete ? (
                                 <Observer>{this.controls}</Observer>
                             ) : (
                                 <LoadingIndicator
diff --git a/src/pages/resultsView/plots/PlotsTabUtils.spec.ts b/src/shared/components/plots/PlotsTabUtils.spec.ts
similarity index 99%
rename from src/pages/resultsView/plots/PlotsTabUtils.spec.ts
rename to src/shared/components/plots/PlotsTabUtils.spec.ts
index 6205d932c77..6d4255869b6 100644
--- a/src/pages/resultsView/plots/PlotsTabUtils.spec.ts
+++ b/src/shared/components/plots/PlotsTabUtils.spec.ts
@@ -32,7 +32,7 @@ import {
     makeAxisLogScaleFunction,
     IAxisData,
     axisHasNegativeNumbers,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+} from './PlotsTabUtils';
 
 import _ from 'lodash';
 import { GenericAssayTypeConstants } from 'shared/lib/GenericAssayUtils/GenericAssayConfig';
diff --git a/src/pages/resultsView/plots/PlotsTabUtils.tsx b/src/shared/components/plots/PlotsTabUtils.tsx
similarity index 99%
rename from src/pages/resultsView/plots/PlotsTabUtils.tsx
rename to src/shared/components/plots/PlotsTabUtils.tsx
index cf377067493..97ba12da992 100644
--- a/src/pages/resultsView/plots/PlotsTabUtils.tsx
+++ b/src/shared/components/plots/PlotsTabUtils.tsx
@@ -3616,3 +3616,16 @@ export function maybeSetLogScale(axisSelection: AxisMenuSelection) {
 export function isGenericAssaySelected(selection: AxisMenuSelection) {
     return selection.genericAssayDataType !== undefined;
 }
+
+export function getOption(
+    option: {
+        value: number;
+        label: string;
+    },
+    profiled: boolean
+) {
+    return {
+        value: option.value,
+        label: profiled ? option.label : option.label + ' (Not profiled)',
+    };
+}
diff --git a/src/pages/resultsView/plots/QuickPlots.spec.ts b/src/shared/components/plots/QuickPlots.spec.ts
similarity index 100%
rename from src/pages/resultsView/plots/QuickPlots.spec.ts
rename to src/shared/components/plots/QuickPlots.spec.ts
diff --git a/src/pages/resultsView/plots/QuickPlots.ts b/src/shared/components/plots/QuickPlots.ts
similarity index 100%
rename from src/pages/resultsView/plots/QuickPlots.ts
rename to src/shared/components/plots/QuickPlots.ts
diff --git a/src/shared/components/plots/ScatterPlot.tsx b/src/shared/components/plots/ScatterPlot.tsx
index e262d11646b..e86837ece64 100644
--- a/src/shared/components/plots/ScatterPlot.tsx
+++ b/src/shared/components/plots/ScatterPlot.tsx
@@ -28,10 +28,7 @@ import {
     getRegressionComputations,
     makeMultilineAxisLabel,
 } from './ScatterPlotUtils';
-import {
-    IAxisLogScaleParams,
-    IPlotSampleData,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+import { IAxisLogScaleParams, IPlotSampleData } from './PlotsTabUtils';
 import ifNotDefined from '../../lib/ifNotDefined';
 import {
     CBIOPORTAL_VICTORY_THEME,
diff --git a/src/shared/components/plots/TablePlot.tsx b/src/shared/components/plots/TablePlot.tsx
index da8d2fa01c1..189fc5c6051 100644
--- a/src/shared/components/plots/TablePlot.tsx
+++ b/src/shared/components/plots/TablePlot.tsx
@@ -10,10 +10,7 @@ import {
     VictoryLegend,
     VictoryScatter,
 } from 'victory';
-import {
-    IStringAxisData,
-    tableCellTextColor,
-} from '../../../pages/resultsView/plots/PlotsTabUtils';
+import { IStringAxisData, tableCellTextColor } from './PlotsTabUtils';
 import { StringListIndexedMap } from '../../lib/ListIndexedMap';
 import naturalSort from 'javascript-natural-sort';
 import * as d3Scale from 'd3-scale';
diff --git a/src/shared/components/plots/TablePlotUtils.ts b/src/shared/components/plots/TablePlotUtils.ts
index ae479eecdfd..ef4991dbd45 100644
--- a/src/shared/components/plots/TablePlotUtils.ts
+++ b/src/shared/components/plots/TablePlotUtils.ts
@@ -1,4 +1,4 @@
-import { IStringAxisData } from '../../../pages/resultsView/plots/PlotsTabUtils';
+import { IStringAxisData } from './PlotsTabUtils';
 import { Sample } from 'cbioportal-ts-api-client';
 function getUniqueSampleKeyToCategories(
     horzData: IStringAxisData['data'],
diff --git a/src/shared/components/plots/WaterfallPlot.spec.tsx b/src/shared/components/plots/WaterfallPlot.spec.tsx
index 7c6014bc1c2..2e96d5c98ca 100644
--- a/src/shared/components/plots/WaterfallPlot.spec.tsx
+++ b/src/shared/components/plots/WaterfallPlot.spec.tsx
@@ -1,5 +1,5 @@
 // need to mock this module to prevent circular references from breaking the tests
-jest.mock('pages/resultsView/plots/PlotsTab.tsx');
+jest.mock('shared/components/plots/PlotsTab.tsx');
 
 import React from 'react';
 import { assert } from 'chai';
diff --git a/src/shared/components/plots/WaterfallPlot.tsx b/src/shared/components/plots/WaterfallPlot.tsx
index a684f7f00d5..20b6f1bc9c4 100644
--- a/src/shared/components/plots/WaterfallPlot.tsx
+++ b/src/shared/components/plots/WaterfallPlot.tsx
@@ -26,7 +26,7 @@ import {
     waterfallSearchIndicatorAppearance,
     limitValueAppearance,
     IValue1D,
-} from 'pages/resultsView/plots/PlotsTabUtils';
+} from './PlotsTabUtils';
 import {
     CBIOPORTAL_VICTORY_THEME,
     baseLabelStyles,
diff --git a/src/pages/resultsView/plots/styles.scss b/src/shared/components/plots/styles.scss
similarity index 100%
rename from src/pages/resultsView/plots/styles.scss
rename to src/shared/components/plots/styles.scss
diff --git a/src/shared/lib/Colors.ts b/src/shared/lib/Colors.ts
index 4913e3dce63..051d8d5eb57 100644
--- a/src/shared/lib/Colors.ts
+++ b/src/shared/lib/Colors.ts
@@ -12,7 +12,6 @@ import {
     MUT_COLOR_TRUNC,
     STRUCTURAL_VARIANT_COLOR,
 } from 'cbioportal-frontend-commons';
-import { MUT_PROFILE_COUNT_NOT_MUTATED } from 'pages/resultsView/plots/PlotsTabUtils';
 import { RGBAColor } from 'oncoprintjs';
 // Default grey
 export const BLACK = '#000000';