From b3687d57a1b93b9cb33c0e45bef997a8b7480221 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:35:50 -0800 Subject: [PATCH 01/17] Chnage page title --- src/DataDeposition/dataDepositionPage.jsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/DataDeposition/dataDepositionPage.jsx b/src/DataDeposition/dataDepositionPage.jsx index 12e0f7f5..017501fd 100644 --- a/src/DataDeposition/dataDepositionPage.jsx +++ b/src/DataDeposition/dataDepositionPage.jsx @@ -8,9 +8,9 @@ function DataDeposition() {
- Data Deposition at Public Repositories - MoTrPAC Data Hub + MoTrPAC Data Accessible at Public Repositories - MoTrPAC Data Hub - +

From 7fc636030d08c33a1e3cf2c58468aac7a8a2db2d Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:44:53 -0800 Subject: [PATCH 02/17] Re-order omes/assays per central dogma E.g. genome, epigenome, trranscriptome, proteome, metabolome (untargeted, targeted) --- src/MainStudy/pass1b06AssayTissueTable.jsx | 32 ++--- src/MainStudy/pass1b_06_assay_tissue.json | 130 ++++++++++----------- 2 files changed, 81 insertions(+), 81 deletions(-) diff --git a/src/MainStudy/pass1b06AssayTissueTable.jsx b/src/MainStudy/pass1b06AssayTissueTable.jsx index 12127e49..69a9eb44 100644 --- a/src/MainStudy/pass1b06AssayTissueTable.jsx +++ b/src/MainStudy/pass1b06AssayTissueTable.jsx @@ -33,8 +33,8 @@ function Pass1b06AssayTissueTable() {

- {/* Render metabolomics-targeted assay table */} -

Targeted Metabolomics

+ {/* Render transcriptomics assay table */} +

Transcriptomics

@@ -44,11 +44,11 @@ function Pass1b06AssayTissueTable() { - {pass1b06AssayByOmicJson['metabolomics-targeted'].map((item) => ( + {pass1b06AssayByOmicJson['transcriptomics'].map((item) => (
{item.assay} - {pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => ( + {pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => ( {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} @@ -59,8 +59,8 @@ function Pass1b06AssayTissueTable() {
- {/* Render metabolomics-untargeted assay table */} -

Untargeted Metabolomics

+ {/* Render proteomics-untargeted assay table */} +

Untargeted Proteomics

@@ -70,11 +70,11 @@ function Pass1b06AssayTissueTable() { - {pass1b06AssayByOmicJson['metabolomics-untargeted'].map((item) => ( + {pass1b06AssayByOmicJson['proteomics-untargeted'].map((item) => (
{item.assay} - {pass1b06AssayTissueJson['metabolomics-untargeted'][item.id].map((tissue) => ( + {pass1b06AssayTissueJson['proteomics-untargeted'][item.id].map((tissue) => ( {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} @@ -85,8 +85,8 @@ function Pass1b06AssayTissueTable() {
- {/* Render proteomics-untargeted assay table */} -

Untargeted Proteomics

+ {/* Render metabolomics-untargeted assay table */} +

Untargeted Metabolomics

@@ -96,11 +96,11 @@ function Pass1b06AssayTissueTable() { - {pass1b06AssayByOmicJson['proteomics-untargeted'].map((item) => ( + {pass1b06AssayByOmicJson['metabolomics-untargeted'].map((item) => (
{item.assay} - {pass1b06AssayTissueJson['proteomics-untargeted'][item.id].map((tissue) => ( + {pass1b06AssayTissueJson['metabolomics-untargeted'][item.id].map((tissue) => ( {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} @@ -111,8 +111,8 @@ function Pass1b06AssayTissueTable() {
- {/* Render transcriptomics assay table */} -

Transcriptomics

+ {/* Render metabolomics-targeted assay table */} +

Targeted Metabolomics

@@ -122,11 +122,11 @@ function Pass1b06AssayTissueTable() { - {pass1b06AssayByOmicJson['transcriptomics'].map((item) => ( + {pass1b06AssayByOmicJson['metabolomics-targeted'].map((item) => (
{item.assay} - {pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => ( + {pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => ( {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} diff --git a/src/MainStudy/pass1b_06_assay_tissue.json b/src/MainStudy/pass1b_06_assay_tissue.json index 1bde6e57..41d5e432 100644 --- a/src/MainStudy/pass1b_06_assay_tissue.json +++ b/src/MainStudy/pass1b_06_assay_tissue.json @@ -21,69 +21,55 @@ "t70-white-adipose" ] }, - "metabolomics-targeted": { - "metab-t-acoa": [ - "t55-gastrocnemius", - "t58-heart", - "t68-liver", - "t70-white-adipose" - ], - "metab-t-amines": [ - "t31-plasma", + "transcriptomics": { + "transcript-rna-seq": [ + "t30-blood-rna", "t52-hippocampus", + "t53-cortex", + "t54-hypothalamus", "t55-gastrocnemius", + "t56-vastus-lateralis", "t58-heart", "t59-kidney", + "t60-adrenal", + "t61-colon", + "t62-spleen", + "t63-testes", + "t64-ovaries", "t66-lung", + "t67-small-intestine", "t68-liver", "t69-brown-adipose", - "t70-white-adipose" + "t70-white-adipose", + "t99-vena-cava" + ] + }, + "proteomics-untargeted": { + "prot-ac": [ + "t58-heart", + "t68-liver" ], - "metab-t-etamidpos": [ - "t31-plasma", - "t52-hippocampus", + "prot-ph": [ + "t53-cortex", "t55-gastrocnemius", "t58-heart", "t59-kidney", "t66-lung", "t68-liver", - "t69-brown-adipose", - "t70-white-adipose" - ], - "metab-t-ka": [ - "t31-plasma", - "t55-gastrocnemius", - "t58-heart", - "t68-liver", - "t70-white-adipose" - ], - "metab-t-nuc": [ - "t55-gastrocnemius", - "t58-heart", - "t68-liver", "t70-white-adipose" ], - "metab-t-oxylipneg": [ - "t31-plasma", - "t52-hippocampus", + "prot-pr": [ + "t53-cortex", "t55-gastrocnemius", "t58-heart", "t59-kidney", "t66-lung", "t68-liver", - "t69-brown-adipose", "t70-white-adipose" ], - "metab-t-tca": [ - "t31-plasma", - "t52-hippocampus", - "t55-gastrocnemius", + "prot-ub": [ "t58-heart", - "t59-kidney", - "t66-lung", - "t68-liver", - "t69-brown-adipose", - "t70-white-adipose" + "t68-liver" ] }, "metabolomics-untargeted": { @@ -164,55 +150,69 @@ "t70-white-adipose" ] }, - "proteomics-untargeted": { - "prot-ac": [ + "metabolomics-targeted": { + "metab-t-acoa": [ + "t55-gastrocnemius", "t58-heart", - "t68-liver" + "t68-liver", + "t70-white-adipose" ], - "prot-ph": [ - "t53-cortex", + "metab-t-amines": [ + "t31-plasma", + "t52-hippocampus", "t55-gastrocnemius", "t58-heart", "t59-kidney", "t66-lung", "t68-liver", + "t69-brown-adipose", "t70-white-adipose" ], - "prot-pr": [ - "t53-cortex", + "metab-t-etamidpos": [ + "t31-plasma", + "t52-hippocampus", "t55-gastrocnemius", "t58-heart", "t59-kidney", "t66-lung", "t68-liver", + "t69-brown-adipose", "t70-white-adipose" ], - "prot-ub": [ + "metab-t-ka": [ + "t31-plasma", + "t55-gastrocnemius", "t58-heart", - "t68-liver" - ] - }, - "transcriptomics": { - "transcript-rna-seq": [ - "t30-blood-rna", + "t68-liver", + "t70-white-adipose" + ], + "metab-t-nuc": [ + "t55-gastrocnemius", + "t58-heart", + "t68-liver", + "t70-white-adipose" + ], + "metab-t-oxylipneg": [ + "t31-plasma", "t52-hippocampus", - "t53-cortex", - "t54-hypothalamus", "t55-gastrocnemius", - "t56-vastus-lateralis", "t58-heart", "t59-kidney", - "t60-adrenal", - "t61-colon", - "t62-spleen", - "t63-testes", - "t64-ovaries", "t66-lung", - "t67-small-intestine", "t68-liver", "t69-brown-adipose", - "t70-white-adipose", - "t99-vena-cava" + "t70-white-adipose" + ], + "metab-t-tca": [ + "t31-plasma", + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" ] } } From cf1523355338f4e8ec97acc6c7c2c250fe95b23b Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:45:41 -0800 Subject: [PATCH 03/17] Add external link to Discoourse community portal --- src/Navbar/navbar.jsx | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx index 2c1ca35e..7c2760ff 100644 --- a/src/Navbar/navbar.jsx +++ b/src/Navbar/navbar.jsx @@ -339,6 +339,14 @@ export function Navbar({ > OmicsPipelines + + Community +
  • From feac74c4bee0acf41164c51cc5d01c8e092326f8 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:50:52 -0800 Subject: [PATCH 04/17] Re-order omes per central dogma: GET, proteome, metabolome --- src/DataDeposition/dataDepositionPage.jsx | 110 +++++++++++----------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/src/DataDeposition/dataDepositionPage.jsx b/src/DataDeposition/dataDepositionPage.jsx index 017501fd..da41de56 100644 --- a/src/DataDeposition/dataDepositionPage.jsx +++ b/src/DataDeposition/dataDepositionPage.jsx @@ -55,61 +55,6 @@ function DataDeposition() {
    • - {/* Immunoassay data deposition table */} -

    Immunoassays

    -
    - - - - - - - - - - - - - - - -
    RepositoryData typeAccession
    - - Readouts, results - -
    -
    - {/* Metabolomics data deposition table */} -

    Metabolomics (Targeted and Untargeted)

    -
    - - - - - - - - - - - - - - - -
    RepositoryData typeProject
    - - Metabolomics raw + results files (identification and quantification) -
      -
    • - -
      • -
    • - -
      • -
    -
    -
    {/* Proteomics data deposition table */}

    Proteomics

    @@ -182,6 +127,61 @@ function DataDeposition() {
    + {/* Immunoassay data deposition table */} +

    Immunoassays

    +
    + + + + + + + + + + + + + + + +
    RepositoryData typeAccession
    + + Readouts, results + +
    +
    + {/* Metabolomics data deposition table */} +

    Metabolomics (Untargeted and Targeted)

    +
    + + + + + + + + + + + + + + + +
    RepositoryData typeProject
    + + Metabolomics raw + results files (identification and quantification) +
      +
    • + +
      • +
    • + +
      • +
    +
    +
    From 0e6a8c8c9c834aab2336d4b29a326210e797005d Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:52:53 -0800 Subject: [PATCH 05/17] Rename data deposition dropdown menu link --- src/Navbar/navbar.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx index 7c2760ff..5b383fa7 100644 --- a/src/Navbar/navbar.jsx +++ b/src/Navbar/navbar.jsx @@ -273,7 +273,7 @@ export function Navbar({ Limited Acute Exercise Data - Data Deposition + Public Data Repositories {!userType || (userType && userType !== 'internal') ? ( Date: Tue, 26 Nov 2024 21:56:02 -0800 Subject: [PATCH 06/17] Add link to phenotype data technical guide page --- src/BrowseDataPage/components/dataDownloadsMain.jsx | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/BrowseDataPage/components/dataDownloadsMain.jsx b/src/BrowseDataPage/components/dataDownloadsMain.jsx index 66e25563..71877835 100644 --- a/src/BrowseDataPage/components/dataDownloadsMain.jsx +++ b/src/BrowseDataPage/components/dataDownloadsMain.jsx @@ -100,8 +100,14 @@ function DataDownloadsMain({

    Study Data

    - Browse and find the data of your interest by tissue, ome, or assay - types. + Browse and customze the data of your interest to download by tissue, + ome, or assay types. It is recommended to download the phenotypic data + along with the omics data for a comprehensive analysis. Learn more + about the + {' '} + phenotypic data + {' '} + in MoTrPAC studies.

    Date: Tue, 26 Nov 2024 21:57:29 -0800 Subject: [PATCH 07/17] Initial commit of example figure for sample data linkage via vial labels and pids --- .../vial_label_data_linkage_example.svg | 183 ++++++++++++++++++ 1 file changed, 183 insertions(+) create mode 100644 src/assets/figures/vial_label_data_linkage_example.svg diff --git a/src/assets/figures/vial_label_data_linkage_example.svg b/src/assets/figures/vial_label_data_linkage_example.svg new file mode 100644 index 00000000..0738007b --- /dev/null +++ b/src/assets/figures/vial_label_data_linkage_example.svg @@ -0,0 +1,183 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ENSRNOG00000000001 + 18.0 + 2.0 + ENSRNOG00000000007 + 10.0 + 6.0 + gene_id + Sample_01a + Sample_02a + + + Compound_01 + 3.5 + 2.0 + Compound_02 + 1.3 + 0.7 + metabolite_name + Sample_01b + Sample_02b + + + Sample_01a + 10029885 + One-week program + 2 + 432 + 58 + -1 + Sample_01b + 10029885 + One-week program + 2 + 432 + 58 + 4 + viallabel(pass1bf0004) + pid(pass1bf0001) + key___ani_rand_group(pass1bf0011) + registration___sex(pass1bf00027) + terminal_weight___mg(pass1bf0058) + vo_2_max_test___vo_2_max_1(pass1bf0056) + calculated_variables___vo_2_max_change(pass1bf0111) + + + + + + + + + + Phenotypic data + RNAseq results + Metabolomics results + \ No newline at end of file From d0c082765b16e4ac13eb619da47bec6e4d0b82ac Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:58:08 -0800 Subject: [PATCH 08/17] Re-order exercise benefit items --- src/MainStudy/exerciseBenefitsData.js | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/MainStudy/exerciseBenefitsData.js b/src/MainStudy/exerciseBenefitsData.js index 3a4c297c..4ddf8070 100644 --- a/src/MainStudy/exerciseBenefitsData.js +++ b/src/MainStudy/exerciseBenefitsData.js @@ -1,4 +1,14 @@ const exerciseBenefitsData = [ + { + title: 'Reduced risk of all-cause mortality', + evidence: 'Regular physical activity is associated with a lower risk of all-cause mortality.', + citationNo: 4, + }, + { + title: 'Reduced risk of cardiovascular diseases', + evidence: 'Exercise reduces the risk of cardiovascular diseases, including heart disease and stroke.', + citationNo: 4, + }, { title: 'Younger-looking skin', evidence: 'Exercise improves skin health by enhancing blood flow and delivering oxygen and nutrients to the skin, promoting collagen production and reducing signs of aging.', @@ -69,16 +79,6 @@ const exerciseBenefitsData = [ evidence: 'Weight-bearing and resistance exercises improve bone density and joint health, reducing the risk of osteoporosis and fractures.', citationNo: 2, }, - { - title: 'Reduced risk of all-cause mortality', - evidence: 'Regular physical activity is associated with a lower risk of all-cause mortality.', - citationNo: 4, - }, - { - title: 'Reduced risk of cardiovascular diseases', - evidence: 'Exercise reduces the risk of cardiovascular diseases, including heart disease and stroke.', - citationNo: 4, - }, { title: 'Improved cognition', evidence: 'Physical activity is linked to better cognitive function and a reduced risk of cognitive decline and dementia.', From acc17786b0ce16a692e754849198f0ef323c549e Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 21:59:06 -0800 Subject: [PATCH 09/17] Initial commit of phenotype data technical guide component --- src/TechnicalGuides/phenotype.jsx | 211 ++++++++++++++++++++++++++++++ src/sass/_technicalGuides.scss | 21 +++ src/sass/main.scss | 1 + 3 files changed, 233 insertions(+) create mode 100644 src/TechnicalGuides/phenotype.jsx create mode 100644 src/sass/_technicalGuides.scss diff --git a/src/TechnicalGuides/phenotype.jsx b/src/TechnicalGuides/phenotype.jsx new file mode 100644 index 00000000..39bd8421 --- /dev/null +++ b/src/TechnicalGuides/phenotype.jsx @@ -0,0 +1,211 @@ +import React from 'react'; +import { Helmet } from 'react-helmet'; +import PageTitle from '../lib/ui/pageTitle'; +import VialLabelExample from '../assets/figures/vial_label_data_linkage_example.svg'; + +/** + * React component that displays the phenotype technical guide. + * + * @returns {React.Component} The phenotype technical guide page. + */ + +function Phenotype() { + return ( +
    + + + Technical Guide: Phenotypic Data - MoTrPAC Data Hub + + +
    +
    +

    + pest_control_rodent + Endurance trained young adult rats study +

    +
    Summary
    +

    + This dataset is a complete collection of measured phenotypic variables, gathered + for a study on Endurance Training in 6-month-old rats. Specifically, male and + female Fischer 344 rats were subjected to progressive treadmill endurance + exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after + the last exercise bout. Sex-matched sedentary, untrained rats were used as + controls. Whole blood, plasma, and 18 solid tissues were analyzed using + epigenomics, transcriptomics, proteomics, metabolomics, and protein immunoassay + technologies, with most assays performed in a subset of these tissues. Depending + on the assay, between 3 and 6 replicates per sex per time point were + analyzed. Although this phenotypic dataset includes 147 animals, a subset of 60 + animals was selected for the molecular assays. +

    +
    Files Overview
    +
    + + description + motrpac_pass1b-06_pheno_viallabel_data_merged_v4.0.txt + +
    +

    + Full collection of phenotypic variables from every biospecimen involved in the + study. It contains multiple variables related to animal tests, registration, + calculations, and specimen processing (as defined in the dictionary file). +

    +

    + Key variables include: +

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    VariableDescription
    viallabel + Vial Label ID. A unique code given to each sample vial. This ID is + found in all related results and metadata files, serving as a key + to match the quantitative results with the phenotypic data. +
    pid + Participant Identifier. Uniquely assigned to each animal subject + (rats in this study). Samples (“viallabel”) coming from the same animal + have the same PID. It is relevant when combining results from multiple + assays and phenotype data. +
    registration___sex + Sex of the animal. 1 = Female, 2 = Male +
    study_group_timepoint + It combines the intervention and sacrifice time codes into a specific + format: [study group (training|control] - [time point (1w|2w|4w|8w weeks)]. +
    specimen_processing___sampletypedescription + Tissue name from which the sample was derived. +
    +
    +
    + + description + motrpac_pass1b-06_pheno_dictionary_merged_v4.0.txt + +
    +

    + This data dictionary defines the scope and possible values of data fields present + in the phenotypic data tables. It is intended to ensure that the phenotypic data + tables are easily interpretable and usable for analysis. +

    +

    + Key variables include: +

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    VariableDescription
    form_name + Groups related variables by the Case Report Form the variable originated from. +
    field_name + Name of specific data field. +
    calculated_or_created_(1=True) + Flag indicating whether the field is calculated. +
    field_description + Description of what the field represents. +
    data_type + Data type of the field (e.g. + {' '} + int + , + {' '} + varchar + , + {' '} + datetime + ). +
    categorical_values + Accepted values for categorical variables. +
    categorical_definitions + Definitions of categorical values. +
    continuous_range_min + Minimum value for continuous variables if applicable. +
    continuous_range_max + Maximum value for continuous variables if applicable. +
    +
    +
    Data Quality Notes
    +

    + Samples from weeks 1 and 2 originating from Vena Cava tissue were excluded + from downstream molecular analysis due to contamination issues. However, + phenotypic data for these samples remains accessible. +

    +
    Example data linkage via vial lables and pids
    +
    + Example data linkage via vial lables and pids +
    +
    +
    +
    + ); +} + +export default Phenotype; diff --git a/src/sass/_technicalGuides.scss b/src/sass/_technicalGuides.scss new file mode 100644 index 00000000..1505f5c7 --- /dev/null +++ b/src/sass/_technicalGuides.scss @@ -0,0 +1,21 @@ +.technicalGuidesPage { + &.phenotype { + .technical-guide-content-container { + h3 { + background: -webkit-linear-gradient(45deg, #a64d79, #1c4587); + -webkit-background-clip: text; + -webkit-text-fill-color: transparent; + + .study-title-species-icon { + font-size: 1.85rem; + } + } + + table { + td:first-child { + width: 35%; + } + } + } + } +} \ No newline at end of file diff --git a/src/sass/main.scss b/src/sass/main.scss index 1c7680b5..508105ef 100644 --- a/src/sass/main.scss +++ b/src/sass/main.scss @@ -41,3 +41,4 @@ @import 'reactLiteYoutubeEmbed'; @import 'license'; @import 'dataDeposition'; +@import 'technicalGuides'; From d6b30d48f269d1b0d6ae5765c823afadb31bee9d Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 22:01:57 -0800 Subject: [PATCH 10/17] Add new public route to phenotype data technical guide --- src/App/App.jsx | 6 ++++++ src/App/__test__/App.test.jsx | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/src/App/App.jsx b/src/App/App.jsx index ac2b5754..ca28af6f 100644 --- a/src/App/App.jsx +++ b/src/App/App.jsx @@ -32,6 +32,7 @@ import Tutorials from '../Tutorials/tutorials'; import License from '../License/licensePage'; import DataDeposition from '../DataDeposition/dataDepositionPage'; import Publications from '../Publications/publications'; +import Phenotype from '../TechnicalGuides/phenotype'; import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups'; import FullTableEnduranceTraining from '../Publications/Data/Animal/Phenotype/fullTableEnduranceTraining'; import Pass1b06PhenotypeAnimalConnected from '../AnalysisPage/pass1b06PhenotypeAnimal'; @@ -159,6 +160,11 @@ function App({ history = History }) { exact component={withTracker(Publications)} /> + ', () => { }); test('It should contain fifteen children', () => { - expect(component.find('Route').length).toBe(25); + expect(component.find('Route').length).toBe(26); }); test('It should contain four children', () => { From 248573ce23816ba3cf3227315d5a97115c306d12 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 26 Nov 2024 22:07:30 -0800 Subject: [PATCH 11/17] Re-order omes per central dogma E.g. genome, epigenome, transcriptome, proteome, metabolome (untargeted, targeted) --- src/MainStudy/pass1b06AssayTissueTreeData.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js index 438496cf..c9b0839b 100644 --- a/src/MainStudy/pass1b06AssayTissueTreeData.js +++ b/src/MainStudy/pass1b06AssayTissueTreeData.js @@ -1,9 +1,9 @@ const pass1b06AssayTissueTreeData = [ [undefined, 'Rats: Endurance Training'], - ['Rats: Endurance Training', 'Transcriptomics'], - ['Rats: Endurance Training', 'Untargeted Proteomics'], - ['Rats: Endurance Training', 'Untargeted Metabolomics'], ['Rats: Endurance Training', 'Targeted Metabolomics'], + ['Rats: Endurance Training', 'Untargeted Metabolomics'], + ['Rats: Endurance Training', 'Untargeted Proteomics'], + ['Rats: Endurance Training', 'Transcriptomics'], ['Rats: Endurance Training', 'Epigenomics'], ['Epigenomics', 'RRBS'], ['Epigenomics', 'ATAC-seq'], From d76e97ea9cdee9c7720bcea159e1bdced4ea2425 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 29 Nov 2024 01:30:40 -0800 Subject: [PATCH 12/17] Remove absolute height of treegraph and set its minHeight to 70vh via CSS due to collapsing most nodes by default --- src/MainStudy/studyAssays.jsx | 5 ++--- src/sass/mainStudy/_mainStudyPage.scss | 4 ++++ 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx index 9c738539..a903f185 100644 --- a/src/MainStudy/studyAssays.jsx +++ b/src/MainStudy/studyAssays.jsx @@ -22,7 +22,6 @@ function StudyAssays() { chart: { spacingBottom: 30, marginRight: 120, - height: 2600, }, title: { align: 'center', @@ -48,7 +47,7 @@ function StudyAssays() { }, dataLabels: { align: 'left', - pointFormat: '{point.id}', + pointFormat: '{point.name}', style: { color: '#000000', textOutline: '3px #ffffff', @@ -115,7 +114,7 @@ function StudyAssays() {
    -
    +

    pest_control_rodent diff --git a/src/sass/mainStudy/_mainStudyPage.scss b/src/sass/mainStudy/_mainStudyPage.scss index 68a11926..a391fb6a 100644 --- a/src/sass/mainStudy/_mainStudyPage.scss +++ b/src/sass/mainStudy/_mainStudyPage.scss @@ -106,6 +106,10 @@ padding: 0.3rem 0.65rem; } } + + .assay-tissue-treegraph-container { + min-height: 70vh; + } } } From 117d338ee87bab78484aabb372b1f0f786a66aa5 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 29 Nov 2024 01:32:35 -0800 Subject: [PATCH 13/17] Reformat treegraph data so that most omic nodes can be set to collapse by default --- src/MainStudy/pass1b06AssayTissueTreeData.js | 403 ++++++++++--------- 1 file changed, 211 insertions(+), 192 deletions(-) diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js index c9b0839b..e48455c9 100644 --- a/src/MainStudy/pass1b06AssayTissueTreeData.js +++ b/src/MainStudy/pass1b06AssayTissueTreeData.js @@ -1,196 +1,215 @@ const pass1b06AssayTissueTreeData = [ - [undefined, 'Rats: Endurance Training'], - ['Rats: Endurance Training', 'Targeted Metabolomics'], - ['Rats: Endurance Training', 'Untargeted Metabolomics'], - ['Rats: Endurance Training', 'Untargeted Proteomics'], - ['Rats: Endurance Training', 'Transcriptomics'], - ['Rats: Endurance Training', 'Epigenomics'], - ['Epigenomics', 'RRBS'], - ['Epigenomics', 'ATAC-seq'], - ['Targeted Metabolomics', 'Targeted Tricarboxylic Acid Cycle'], - ['Targeted Metabolomics', 'Targeted Oxylipins'], - ['Targeted Metabolomics', 'Targeted Nucleotides'], - ['Targeted Metabolomics', 'Targeted Keto Acids'], - ['Targeted Metabolomics', 'Targeted Ethanolamides'], - ['Targeted Metabolomics', 'Targeted Amines'], - ['Targeted Metabolomics', 'Targeted Acyl-CoA'], - ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Positive'], - ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Negative'], - ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Positive'], - ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Negative'], - ['Untargeted Metabolomics', 'Untargeted Ion-Pair Negative'], - ['Untargeted Metabolomics', 'Untargeted HILIC-Positive'], - ['Untargeted Proteomics', 'Protein Ubiquitination'], - ['Untargeted Proteomics', 'Global Proteomics'], - ['Untargeted Proteomics', 'Phosphoproteomics'], - ['Untargeted Proteomics', 'Acetyl Proteomics'], - ['Transcriptomics', 'RNA-seq'], - ['ATAC-seq', 'White Adipose'], - ['ATAC-seq', 'Brown Adipose'], - ['ATAC-seq', 'Liver'], - ['ATAC-seq', 'Lung'], - ['ATAC-seq', 'Kidney'], - ['ATAC-seq', 'Heart'], - ['ATAC-seq', 'Gastrocnemius'], - ['ATAC-seq', 'Hippocampus'], - ['RRBS', 'White Adipose'], - ['RRBS', 'Brown Adipose'], - ['RRBS', 'Liver'], - ['RRBS', 'Lung'], - ['RRBS', 'Kidney'], - ['RRBS', 'Heart'], - ['RRBS', 'Gastrocnemius'], - ['RRBS', 'Hippocampus'], - ['Targeted Tricarboxylic Acid Cycle', 'White Adipose'], - ['Targeted Tricarboxylic Acid Cycle', 'Brown Adipose'], - ['Targeted Tricarboxylic Acid Cycle', 'Liver'], - ['Targeted Tricarboxylic Acid Cycle', 'Lung'], - ['Targeted Tricarboxylic Acid Cycle', 'Kidney'], - ['Targeted Tricarboxylic Acid Cycle', 'Heart'], - ['Targeted Tricarboxylic Acid Cycle', 'Gastrocnemius'], - ['Targeted Tricarboxylic Acid Cycle', 'Hippocampus'], - ['Targeted Tricarboxylic Acid Cycle', 'Plasma'], - ['Targeted Oxylipins', 'White Adipose'], - ['Targeted Oxylipins', 'Brown Adipose'], - ['Targeted Oxylipins', 'Liver'], - ['Targeted Oxylipins', 'Lung'], - ['Targeted Oxylipins', 'Kidney'], - ['Targeted Oxylipins', 'Heart'], - ['Targeted Oxylipins', 'Gastrocnemius'], - ['Targeted Oxylipins', 'Hippocampus'], - ['Targeted Oxylipins', 'Plasma'], - ['Targeted Nucleotides', 'White Adipose'], - ['Targeted Nucleotides', 'Liver'], - ['Targeted Nucleotides', 'Heart'], - ['Targeted Nucleotides', 'Gastrocnemius'], - ['Targeted Keto Acids', 'White Adipose'], - ['Targeted Keto Acids', 'Liver'], - ['Targeted Keto Acids', 'Heart'], - ['Targeted Keto Acids', 'Gastrocnemius'], - ['Targeted Keto Acids', 'Plasma'], - ['Targeted Ethanolamides', 'White Adipose'], - ['Targeted Ethanolamides', 'Brown Adipose'], - ['Targeted Ethanolamides', 'Liver'], - ['Targeted Ethanolamides', 'Lung'], - ['Targeted Ethanolamides', 'Kidney'], - ['Targeted Ethanolamides', 'Heart'], - ['Targeted Ethanolamides', 'Gastrocnemius'], - ['Targeted Ethanolamides', 'Hippocampus'], - ['Targeted Ethanolamides', 'Plasma'], - ['Targeted Amines', 'White Adipose'], - ['Targeted Amines', 'Brown Adipose'], - ['Targeted Amines', 'Liver'], - ['Targeted Amines', 'Lung'], - ['Targeted Amines', 'Kidney'], - ['Targeted Amines', 'Heart'], - ['Targeted Amines', 'Gastrocnemius'], - ['Targeted Amines', 'Hippocampus'], - ['Targeted Amines', 'Plasma'], - ['Targeted Acyl-CoA', 'White Adipose'], - ['Targeted Acyl-CoA', 'Liver'], - ['Targeted Acyl-CoA', 'Heart'], - ['Targeted Acyl-CoA', 'Gastrocnemius'], - ['Untargeted Reversed-Phase Positive', 'White Adipose'], - ['Untargeted Reversed-Phase Positive', 'Brown Adipose'], - ['Untargeted Reversed-Phase Positive', 'Liver'], - ['Untargeted Reversed-Phase Positive', 'Lung'], - ['Untargeted Reversed-Phase Positive', 'Kidney'], - ['Untargeted Reversed-Phase Positive', 'Heart'], - ['Untargeted Reversed-Phase Positive', 'Gastrocnemius'], - ['Untargeted Reversed-Phase Positive', 'Hippocampus'], - ['Untargeted Reversed-Phase Positive', 'Plasma'], - ['Untargeted Reversed-Phase Negative', 'White Adipose'], - ['Untargeted Reversed-Phase Negative', 'Brown Adipose'], - ['Untargeted Reversed-Phase Negative', 'Liver'], - ['Untargeted Reversed-Phase Negative', 'Lung'], - ['Untargeted Reversed-Phase Negative', 'Kidney'], - ['Untargeted Reversed-Phase Negative', 'Heart'], - ['Untargeted Reversed-Phase Negative', 'Gastrocnemius'], - ['Untargeted Reversed-Phase Negative', 'Hippocampus'], - ['Untargeted Reversed-Phase Negative', 'Plasma'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'White Adipose'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Brown Adipose'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Liver'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Lung'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Kidney'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Heart'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Gastrocnemius'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Hippocampus'], - ['Untargeted Lipidomics Reversed-Phase Positive', 'Plasma'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'White Adipose'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Brown Adipose'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Liver'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Lung'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Kidney'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Heart'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Gastrocnemius'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Hippocampus'], - ['Untargeted Lipidomics Reversed-Phase Negative', 'Plasma'], - ['Untargeted Ion-Pair Negative', 'White Adipose'], - ['Untargeted Ion-Pair Negative', 'Brown Adipose'], - ['Untargeted Ion-Pair Negative', 'Liver'], - ['Untargeted Ion-Pair Negative', 'Lung'], - ['Untargeted Ion-Pair Negative', 'Kidney'], - ['Untargeted Ion-Pair Negative', 'Heart'], - ['Untargeted Ion-Pair Negative', 'Gastrocnemius'], - ['Untargeted Ion-Pair Negative', 'Hippocampus'], - ['Untargeted Ion-Pair Negative', 'Plasma'], - ['Untargeted HILIC-Positive', 'Vena Cava'], - ['Untargeted HILIC-Positive', 'White Adipose'], - ['Untargeted HILIC-Positive', 'Brown Adipose'], - ['Untargeted HILIC-Positive', 'Liver'], - ['Untargeted HILIC-Positive', 'Small Intestine'], - ['Untargeted HILIC-Positive', 'Lung'], - ['Untargeted HILIC-Positive', 'Ovaries'], - ['Untargeted HILIC-Positive', 'Testes'], - ['Untargeted HILIC-Positive', 'Spleen'], - ['Untargeted HILIC-Positive', 'Colon'], - ['Untargeted HILIC-Positive', 'Adrenal'], - ['Untargeted HILIC-Positive', 'Kidney'], - ['Untargeted HILIC-Positive', 'Heart'], - ['Untargeted HILIC-Positive', 'Vastus Lateralis'], - ['Untargeted HILIC-Positive', 'Gastrocnemius'], - ['Untargeted HILIC-Positive', 'Hypothalamus'], - ['Untargeted HILIC-Positive', 'Cortex'], - ['Untargeted HILIC-Positive', 'Hippocampus'], - ['Untargeted HILIC-Positive', 'Plasma'], - ['Protein Ubiquitination', 'Liver'], - ['Protein Ubiquitination', 'Heart'], - ['Global Proteomics', 'White Adipose'], - ['Global Proteomics', 'Liver'], - ['Global Proteomics', 'Lung'], - ['Global Proteomics', 'Kidney'], - ['Global Proteomics', 'Heart'], - ['Global Proteomics', 'Gastrocnemius'], - ['Global Proteomics', 'Cortex'], - ['Phosphoproteomics', 'White Adipose'], - ['Phosphoproteomics', 'Liver'], - ['Phosphoproteomics', 'Lung'], - ['Phosphoproteomics', 'Kidney'], - ['Phosphoproteomics', 'Heart'], - ['Phosphoproteomics', 'Gastrocnemius'], - ['Phosphoproteomics', 'Cortex'], - ['Acetyl Proteomics', 'Liver'], - ['Acetyl Proteomics', 'Heart'], - ['RNA-seq', 'Vena Cava'], - ['RNA-seq', 'White Adipose'], - ['RNA-seq', 'Brown Adipose'], - ['RNA-seq', 'Liver'], - ['RNA-seq', 'Small Intestine'], - ['RNA-seq', 'Lung'], - ['RNA-seq', 'Ovaries'], - ['RNA-seq', 'Testes'], - ['RNA-seq', 'Spleen'], - ['RNA-seq', 'Colon'], - ['RNA-seq', 'Adrenal'], - ['RNA-seq', 'Kidney'], - ['RNA-seq', 'Heart'], - ['RNA-seq', 'Vastus Lateralis'], - ['RNA-seq', 'Gastrocnemius'], - ['RNA-seq', 'Hypothalamus'], - ['RNA-seq', 'Cortex'], - ['RNA-seq', 'Hippocampus'], - ['RNA-seq', 'Blood Rna'], + { id: '0.0', parent: '', name: 'Rats: Endurance Training' }, + { id: '1.0', parent: '0.0', name: 'Targeted Metabolomics', collapsed: true }, + { id: '1.1', parent: '0.0', name: 'Untargeted Metabolomics', collapsed: true }, + { id: '1.2', parent: '0.0', name: 'Untargeted Proteomics', collapsed: true }, + { id: '1.3', parent: '0.0', name: 'Transcriptomics' }, + { id: '1.4', parent: '0.0', name: 'Epigenomics', collapsed: true }, + { id: '2.0', parent: '1.4', name: 'RRBS' }, + { id: '2.1', parent: '1.4', name: 'ATAC-seq' }, + { id: '2.2', parent: '1.0', name: 'Targeted Tricarboxylic Acid Cycle' }, + { id: '2.3', parent: '1.0', name: 'Targeted Oxylipins' }, + { id: '2.4', parent: '1.0', name: 'Targeted Nucleotides' }, + { id: '2.5', parent: '1.0', name: 'Targeted Keto Acids' }, + { id: '2.6', parent: '1.0', name: 'Targeted Ethanolamides' }, + { id: '2.7', parent: '1.0', name: 'Targeted Amines' }, + { id: '2.8', parent: '1.0', name: 'Targeted Acyl-CoA' }, + { id: '2.9', parent: '1.1', name: 'Untargeted Reversed-Phase Positive' }, + { id: '2.10', parent: '1.1', name: 'Untargeted Reversed-Phase Negative' }, + { id: '2.11', parent: '1.1', name: 'Untargeted Lipidomics Reversed-Phase Positive' }, + { id: '2.12', parent: '1.1', name: 'Untargeted Lipidomics Reversed-Phase Negative' }, + { id: '2.13', parent: '1.1', name: 'Untargeted Ion-Pair Negative' }, + { id: '2.14', parent: '1.1', name: 'Untargeted HILIC-Positive' }, + { id: '2.15', parent: '1.2', name: 'Protein Ubiquitination' }, + { id: '2.16', parent: '1.2', name: 'Global Proteomics' }, + { id: '2.17', parent: '1.2', name: 'Phosphoproteomics' }, + { id: '2.18', parent: '1.2', name: 'Acetyl Proteomics' }, + { id: '2.19', parent: '1.3', name: 'RNA-seq' }, + // RRBS tissues + { id: '3.0', parent: '2.0', name: 'White Adipose' }, + { id: '3.1', parent: '2.0', name: 'Brown Adipose' }, + { id: '3.2', parent: '2.0', name: 'Liver' }, + { id: '3.3', parent: '2.0', name: 'Lung' }, + { id: '3.4', parent: '2.0', name: 'Kidney' }, + { id: '3.5', parent: '2.0', name: 'Heart' }, + { id: '3.6', parent: '2.0', name: 'Gastrocnemius' }, + { id: '3.7', parent: '2.0', name: 'Hippocampus' }, + // ATAC-seq tissues + { id: '3.8', parent: '2.1', name: 'White Adipose' }, + { id: '3.9', parent: '2.1', name: 'Brown Adipose' }, + { id: '3.10', parent: '2.1', name: 'Liver' }, + { id: '3.11', parent: '2.1', name: 'Lung' }, + { id: '3.12', parent: '2.1', name: 'Kidney' }, + { id: '3.13', parent: '2.1', name: 'Heart' }, + { id: '3.14', parent: '2.1', name: 'Gastrocnemius' }, + { id: '3.15', parent: '2.1', name: 'Hippocampus' }, + // Targeted Tricarboxylic Acid Cycle tissues + { id: '3.16', parent: '2.2', name: 'White Adipose' }, + { id: '3.17', parent: '2.2', name: 'Brown Adipose' }, + { id: '3.18', parent: '2.2', name: 'Liver' }, + { id: '3.19', parent: '2.2', name: 'Lung' }, + { id: '3.20', parent: '2.2', name: 'Kidney' }, + { id: '3.21', parent: '2.2', name: 'Heart' }, + { id: '3.22', parent: '2.2', name: 'Gastrocnemius' }, + { id: '3.23', parent: '2.2', name: 'Hippocampus' }, + { id: '3.24', parent: '2.2', name: 'Plasma' }, + // Targeted Oxylipins tissues + { id: '3.25', parent: '2.3', name: 'White Adipose' }, + { id: '3.26', parent: '2.3', name: 'Brown Adipose' }, + { id: '3.27', parent: '2.3', name: 'Liver' }, + { id: '3.28', parent: '2.3', name: 'Lung' }, + { id: '3.29', parent: '2.3', name: 'Kidney' }, + { id: '3.30', parent: '2.3', name: 'Heart' }, + { id: '3.31', parent: '2.3', name: 'Gastrocnemius' }, + { id: '3.32', parent: '2.3', name: 'Hippocampus' }, + { id: '3.33', parent: '2.3', name: 'Plasma' }, + // Targeted Nucleotides tissues + { id: '3.34', parent: '2.4', name: 'White Adipose' }, + { id: '3.35', parent: '2.4', name: 'Liver' }, + { id: '3.36', parent: '2.4', name: 'Heart' }, + { id: '3.37', parent: '2.4', name: 'Gastrocnemius' }, + // Targeted Keto Acids tissues + { id: '3.38', parent: '2.5', name: 'White Adipose' }, + { id: '3.39', parent: '2.5', name: 'Liver' }, + { id: '3.40', parent: '2.5', name: 'Heart' }, + { id: '3.41', parent: '2.5', name: 'Gastrocnemius' }, + { id: '3.42', parent: '2.5', name: 'Plasma' }, + // Targeted Ethanolamides tissues + { id: '3.43', parent: '2.6', name: 'White Adipose' }, + { id: '3.44', parent: '2.6', name: 'Brown Adipose' }, + { id: '3.45', parent: '2.6', name: 'Liver' }, + { id: '3.46', parent: '2.6', name: 'Lung' }, + { id: '3.47', parent: '2.6', name: 'Kidney' }, + { id: '3.48', parent: '2.6', name: 'Heart' }, + { id: '3.49', parent: '2.6', name: 'Gastrocnemius' }, + { id: '3.50', parent: '2.6', name: 'Hippocampus' }, + { id: '3.51', parent: '2.6', name: 'Plasma' }, + // Targeted Amines tissues + { id: '3.52', parent: '2.7', name: 'White Adipose' }, + { id: '3.53', parent: '2.7', name: 'Brown Adipose' }, + { id: '3.54', parent: '2.7', name: 'Liver' }, + { id: '3.55', parent: '2.7', name: 'Lung' }, + { id: '3.56', parent: '2.7', name: 'Kidney' }, + { id: '3.57', parent: '2.7', name: 'Heart' }, + { id: '3.58', parent: '2.7', name: 'Gastrocnemius' }, + { id: '3.59', parent: '2.7', name: 'Hippocampus' }, + { id: '3.60', parent: '2.7', name: 'Plasma' }, + // Targeted Acyl-CoA tissues + { id: '3.61', parent: '2.8', name: 'White Adipose' }, + { id: '3.62', parent: '2.8', name: 'Liver' }, + { id: '3.63', parent: '2.8', name: 'Heart' }, + { id: '3.64', parent: '2.8', name: 'Gastrocnemius' }, + // Untargeted Reversed-Phase Positive tissues + { id: '3.65', parent: '2.9', name: 'White Adipose' }, + { id: '3.66', parent: '2.9', name: 'Brown Adipose' }, + { id: '3.67', parent: '2.9', name: 'Liver' }, + { id: '3.68', parent: '2.9', name: 'Lung' }, + { id: '3.69', parent: '2.9', name: 'Kidney' }, + { id: '3.70', parent: '2.9', name: 'Heart' }, + { id: '3.71', parent: '2.9', name: 'Gastrocnemius' }, + { id: '3.72', parent: '2.9', name: 'Hippocampus' }, + { id: '3.73', parent: '2.9', name: 'Plasma' }, + // Untargeted Reversed-Phase Negative tissues + { id: '3.74', parent: '2.10', name: 'White Adipose' }, + { id: '3.75', parent: '2.10', name: 'Brown Adipose' }, + { id: '3.76', parent: '2.10', name: 'Liver' }, + { id: '3.77', parent: '2.10', name: 'Lung' }, + { id: '3.78', parent: '2.10', name: 'Kidney' }, + { id: '3.79', parent: '2.10', name: 'Heart' }, + { id: '3.80', parent: '2.10', name: 'Gastrocnemius' }, + { id: '3.81', parent: '2.10', name: 'Hippocampus' }, + { id: '3.82', parent: '2.10', name: 'Plasma' }, + // Untargeted Lipidomics Reversed-Phase Positive tissues + { id: '3.83', parent: '2.11', name: 'White Adipose' }, + { id: '3.84', parent: '2.11', name: 'Brown Adipose' }, + { id: '3.85', parent: '2.11', name: 'Liver' }, + { id: '3.86', parent: '2.11', name: 'Lung' }, + { id: '3.87', parent: '2.11', name: 'Kidney' }, + { id: '3.88', parent: '2.11', name: 'Heart' }, + { id: '3.89', parent: '2.11', name: 'Gastrocnemius' }, + { id: '3.90', parent: '2.11', name: 'Hippocampus' }, + { id: '3.91', parent: '2.11', name: 'Plasma' }, + // Untargeted Lipidomics Reversed-Phase Negaive tissues + { id: '3.92', parent: '2.12', name: 'White Adipose' }, + { id: '3.93', parent: '2.12', name: 'Brown Adipose' }, + { id: '3.94', parent: '2.12', name: 'Liver' }, + { id: '3.95', parent: '2.12', name: 'Lung' }, + { id: '3.96', parent: '2.12', name: 'Kidney' }, + { id: '3.97', parent: '2.12', name: 'Heart' }, + { id: '3.98', parent: '2.12', name: 'Gastrocnemius' }, + { id: '3.99', parent: '2.12', name: 'Hippocampus' }, + { id: '4.00', parent: '2.12', name: 'Plasma' }, + // Untargeted Ion-Pair Negative tissues + { id: '4.01', parent: '2.13', name: 'White Adipose' }, + { id: '4.02', parent: '2.13', name: 'Brown Adipose' }, + { id: '4.03', parent: '2.13', name: 'Liver' }, + { id: '4.04', parent: '2.13', name: 'Lung' }, + { id: '4.05', parent: '2.13', name: 'Kidney' }, + { id: '4.06', parent: '2.13', name: 'Heart' }, + { id: '4.07', parent: '2.13', name: 'Gastrocnemius' }, + { id: '4.08', parent: '2.13', name: 'Hippocampus' }, + { id: '4.09', parent: '2.13', name: 'Plasma' }, + // Untargeted HILIC-Positive tissues + { id: '4.10', parent: '2.14', name: 'White Adipose' }, + { id: '4.11', parent: '2.14', name: 'Brown Adipose' }, + { id: '4.12', parent: '2.14', name: 'Liver' }, + { id: '4.12', parent: '2.14', name: 'Small Intestine' }, + { id: '4.14', parent: '2.14', name: 'Lung' }, + { id: '4.15', parent: '2.14', name: 'Ovaries' }, + { id: '4.16', parent: '2.14', name: 'Testes' }, + { id: '4.17', parent: '2.14', name: 'Spleen' }, + { id: '4.18', parent: '2.14', name: 'Colon' }, + { id: '4.19', parent: '2.14', name: 'Adrenal' }, + { id: '4.20', parent: '2.14', name: 'Kidney' }, + { id: '4.21', parent: '2.14', name: 'Heart' }, + { id: '4.22', parent: '2.14', name: 'Vastus Lateralis' }, + { id: '4.23', parent: '2.14', name: 'Gastrocnemius' }, + { id: '4.24', parent: '2.14', name: 'Hypothalamus' }, + { id: '4.25', parent: '2.14', name: 'Cortex' }, + { id: '4.26', parent: '2.14', name: 'Hippocampus' }, + { id: '4.27', parent: '2.14', name: 'Plasma' }, + // Protein Ubiquitination tissues + { id: '4.28', parent: '2.15', name: 'Liver' }, + { id: '4.29', parent: '2.15', name: 'Heart' }, + // Global Proteomics tissues + { id: '4.30', parent: '2.16', name: 'White Adipose' }, + { id: '4.31', parent: '2.16', name: 'Liver' }, + { id: '4.32', parent: '2.16', name: 'Lung' }, + { id: '4.33', parent: '2.16', name: 'Kidney' }, + { id: '4.34', parent: '2.16', name: 'Heart' }, + { id: '4.35', parent: '2.16', name: 'Gastrocnemius' }, + { id: '4.36', parent: '2.16', name: 'Cortex' }, + // Phosphoproteomics tissues + { id: '4.37', parent: '2.17', name: 'White Adipose' }, + { id: '4.38', parent: '2.17', name: 'Liver' }, + { id: '4.39', parent: '2.17', name: 'Lung' }, + { id: '4.41', parent: '2.17', name: 'Kidney' }, + { id: '4.42', parent: '2.17', name: 'Heart' }, + { id: '4.43', parent: '2.17', name: 'Gastrocnemius' }, + { id: '4.44', parent: '2.17', name: 'Cortex' }, + // Acetyl Proteomics tissues + { id: '4.45', parent: '2.18', name: 'Liver' }, + { id: '4.46', parent: '2.18', name: 'Heart' }, + // Untargeted HILIC-Positive tissues + { id: '4.47', parent: '2.19', name: 'Vena Cava' }, + { id: '4.48', parent: '2.19', name: 'White Adipose' }, + { id: '4.49', parent: '2.19', name: 'Brown Adipose' }, + { id: '4.50', parent: '2.19', name: 'Liver' }, + { id: '4.51', parent: '2.19', name: 'Small Intestine' }, + { id: '4.52', parent: '2.19', name: 'Lung' }, + { id: '4.53', parent: '2.19', name: 'Ovaries' }, + { id: '4.54', parent: '2.19', name: 'Testes' }, + { id: '4.55', parent: '2.19', name: 'Spleen' }, + { id: '4.56', parent: '2.19', name: 'Colon' }, + { id: '4.57', parent: '2.19', name: 'Adrenal' }, + { id: '4.58', parent: '2.19', name: 'Kidney' }, + { id: '4.59', parent: '2.19', name: 'Heart' }, + { id: '4.60', parent: '2.19', name: 'Vastus Lateralis' }, + { id: '4.61', parent: '2.19', name: 'Gastrocnemius' }, + { id: '4.62', parent: '2.19', name: 'Hypothalamus' }, + { id: '4.63', parent: '2.19', name: 'Cortex' }, + { id: '4.64', parent: '2.19', name: 'Hippocampus' }, + { id: '4.65', parent: '2.19', name: 'Blood Rna' }, ]; export default pass1b06AssayTissueTreeData; From c15c40cc5bc52ac78f50d530508caa4003699f7e Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Sat, 30 Nov 2024 01:14:34 -0800 Subject: [PATCH 14/17] Fix typo --- src/TechnicalGuides/phenotype.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/TechnicalGuides/phenotype.jsx b/src/TechnicalGuides/phenotype.jsx index 39bd8421..f26dc093 100644 --- a/src/TechnicalGuides/phenotype.jsx +++ b/src/TechnicalGuides/phenotype.jsx @@ -195,7 +195,7 @@ function Phenotype() { from downstream molecular analysis due to contamination issues. However, phenotypic data for these samples remains accessible.

    -
    Example data linkage via vial lables and pids
    +
    Example data linkage via vial labels and pids
    Date: Mon, 2 Dec 2024 12:36:39 -0800 Subject: [PATCH 15/17] Update example figure --- .../vial_label_data_linkage_example.svg | 242 +++++++++--------- 1 file changed, 121 insertions(+), 121 deletions(-) diff --git a/src/assets/figures/vial_label_data_linkage_example.svg b/src/assets/figures/vial_label_data_linkage_example.svg index 0738007b..ccc6254e 100644 --- a/src/assets/figures/vial_label_data_linkage_example.svg +++ b/src/assets/figures/vial_label_data_linkage_example.svg @@ -1,183 +1,183 @@ - + - - - - - - - - - + + + + + + + + + - - - - - - - - - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - ENSRNOG00000000001 - 18.0 - 2.0 - ENSRNOG00000000007 - 10.0 - 6.0 - gene_id - Sample_01a - Sample_02a + ENSRNOG00000000001 + 18.0 + 2.0 + ENSRNOG00000000007 + 10.0 + 6.0 + gene_id + Sample_01a + Sample_02a - Compound_01 - 3.5 - 2.0 - Compound_02 - 1.3 - 0.7 - metabolite_name - Sample_01b - Sample_02b + Compound_01 + 3.5 + 2.0 + Compound_02 + 1.3 + 0.7 + metabolite_name + Sample_01b + Sample_02b - Sample_01a - 10029885 - One-week program - 2 - 432 - 58 - -1 - Sample_01b - 10029885 - One-week program - 2 - 432 - 58 - 4 - viallabel(pass1bf0004) - pid(pass1bf0001) - key___ani_rand_group(pass1bf0011) - registration___sex(pass1bf00027) - terminal_weight___mg(pass1bf0058) - vo_2_max_test___vo_2_max_1(pass1bf0056) - calculated_variables___vo_2_max_change(pass1bf0111) + Sample_01a + 10029885 + One-week program + 2 + 432 + 58 + -1 + Sample_01b + 10029885 + One-week program + 2 + 432 + 58 + 4 + viallabel + pid + key___ani_rand_group + registration___sex + terminal_weight___mg + vo_2_max_test___vo_2_max_1 + calculated_variables___vo_2_max_change - - - - - - + + + + + + - Phenotypic data - RNAseq results - Metabolomics results + Phenotypic data + RNAseq results + Metabolomics results \ No newline at end of file From d345d49c3c03bd666c84f004561e1d380ec29c97 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 2 Dec 2024 13:54:10 -0800 Subject: [PATCH 16/17] Additional update on example figure --- .../vial_label_data_linkage_example.svg | 198 +++++++++--------- 1 file changed, 102 insertions(+), 96 deletions(-) diff --git a/src/assets/figures/vial_label_data_linkage_example.svg b/src/assets/figures/vial_label_data_linkage_example.svg index ccc6254e..66e52345 100644 --- a/src/assets/figures/vial_label_data_linkage_example.svg +++ b/src/assets/figures/vial_label_data_linkage_example.svg @@ -1,5 +1,5 @@ - + - - - - - - - - - + + + + + + + + + - - - - - - - - - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - ENSRNOG00000000001 - 18.0 - 2.0 - ENSRNOG00000000007 - 10.0 - 6.0 - gene_id - Sample_01a - Sample_02a + ENSRNOG00000000001 + 18.0 + 2.0 + ENSRNOG00000000007 + 10.0 + 6.0 + gene_id + Sample_01a + Sample_02a - Compound_01 - 3.5 - 2.0 - Compound_02 - 1.3 - 0.7 - metabolite_name - Sample_01b - Sample_02b + Compound_01 + 3.5 + 2.0 + Compound_02 + 1.3 + 0.7 + metabolite_name + Sample_01b + Sample_02b - Sample_01a - 10029885 - One-week program - 2 - 432 - 58 - -1 - Sample_01b - 10029885 - One-week program - 2 - 432 - 58 - 4 - viallabel - pid - key___ani_rand_group - registration___sex - terminal_weight___mg - vo_2_max_test___vo_2_max_1 - calculated_variables___vo_2_max_change + Sample_01a + 10029885 + One-week program + 2 + 432 + 58 + -1 + Sample_01b + 10029885 + One-week program + 2 + 432 + 58 + 4 + viallabel + pid + key___ani_rand_group + registration___sex + terminal_weight___mg + vo_2_max_test___vo_2_max_1 + calculated_variables___vo_2_max_change - - - - - - + + + + + + - Phenotypic data - RNAseq results - Metabolomics results + Phenotypic data + RNA-seq results + Metabolomics results \ No newline at end of file From 0c7ea12014977bc3f17b5b6e3ad9d366e80d422c Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 2 Dec 2024 14:26:33 -0800 Subject: [PATCH 17/17] Fix typo --- src/BrowseDataPage/components/dataDownloadsMain.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/BrowseDataPage/components/dataDownloadsMain.jsx b/src/BrowseDataPage/components/dataDownloadsMain.jsx index 71877835..f301adae 100644 --- a/src/BrowseDataPage/components/dataDownloadsMain.jsx +++ b/src/BrowseDataPage/components/dataDownloadsMain.jsx @@ -100,7 +100,7 @@ function DataDownloadsMain({

    Study Data

    - Browse and customze the data of your interest to download by tissue, + Browse and customize the data of your interest to download by tissue, ome, or assay types. It is recommended to download the phenotypic data along with the omics data for a comprehensive analysis. Learn more about the