Merge pull request #802 from josschavezf/suite_modular

add vignettes
drieslab · Nov 20, 2023 · 7be188b · 7be188b
2 parents 9d404f4 + a25960f
commit 7be188b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,4 @@
 .Rbuildignore.save
 ^\.github$
 ^codecov\.yml$
+^vignettes$
diff --git a/NEWS.md b/NEWS.md
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -13,22 +13,89 @@ template:
     primary: "#7E69AE"
     code_font: {google: "JetBrains Mono"}
 
+development:
+  mode: auto
+
 navbar:
   bg: dark
   structure:
     left:
     - intro
     - reference
-    right: github
+    - articles
+    - news
+    right:
+    - search
+    - github
   components:
     reference:
       text: Documentation
       href: reference/index.html
+    articles:
+      text: Tutorials
+      menu:
+      - text: Stereo-seq
+      - text: MOSTA E12.5_E1S3
+        href: articles/stereoseq_mosta.html
+      - text: -------
+      - text: Seq-Scope
+      - text: Mouse liver
+        href: articles/seqscope_mouse_liver.html
+      - text: -------
+      - text: Visium
+      - text: Visium Mouse Kidney
+        href: articles/visium_mouse_kidney.html
+      - text: Visium Mouse Brain
+        href: articles/visium_mouse_brain.html
+      - text: Visium Prostate Integration
+        href: articles/visium_prostate_integration.html
+      - text: CytAssist Human Lung Cancer
+        href: articles/visium_cytassist_lungcancer.html
+      - text: CytAssist Multi-omics Human Glioblastoma
+        href: articles/visium_cytassist_human_glioblastoma.html
+      - text: -------
+      - text: Single Cell RNA Sequencing
+      - text: Prostate
+        href: articles/singlecell_prostate_standard.html
+      - text: Prostate Integration
+        href: articles/singlecell_prostate_integration.html
+    news:
+      text: News
+      href: news/index.html
     github:
       icon: fab fa-github fa-lg
       href: https://github.com/drieslab/Giotto/
       aria-label: github
 
+articles:
+- title: Stereo-seq
+  navbar: ~
+  contents:
+  - stereoseq_mosta
+- title: Seq-Scope
+  navbar: ~
+  contents:
+  - seqscope_mouse_liver
+- title: Visium
+  navbar: ~
+  contents:
+  - visium_mouse_kidney
+  - visium_mouse_brain
+  - visium_prostate_integration
+  - visium_cytassist_lungcancer
+  - visium_cytassist_human_glioblastoma
+- title: Single Cell RNA Sequencing
+  navbar: ~
+  contents:
+  - singlecell_prostate_standard
+  - singlecell_prostate_integration
+
+
+
+news:
+  cran_dates: false
+
+
 home:
   sidebar:
     structure: [links, license, community, citation, authors, dev]
diff --git a/vignettes/images/general_figs/CODEX_spleen_image_summary.png b/vignettes/images/general_figs/CODEX_spleen_image_summary.png
diff --git a/vignettes/images/general_figs/Giotto_to_suite.png b/vignettes/images/general_figs/Giotto_to_suite.png
diff --git a/vignettes/images/general_figs/Visium_FFPE_Human_Normal_Prostate_image.png b/vignettes/images/general_figs/Visium_FFPE_Human_Normal_Prostate_image.png
diff --git a/vignettes/images/general_figs/Visium_FFPE_Human_Prostate_Cancer_image.png b/vignettes/images/general_figs/Visium_FFPE_Human_Prostate_Cancer_image.png
diff --git a/vignettes/images/general_figs/coming_soon_summary.png b/vignettes/images/general_figs/coming_soon_summary.png
diff --git a/vignettes/images/general_figs/construction-boy.png b/vignettes/images/general_figs/construction-boy.png
diff --git a/vignettes/images/general_figs/cortex_image_summary.png b/vignettes/images/general_figs/cortex_image_summary.png
diff --git a/vignettes/images/general_figs/cortex_svz_location_fields.png b/vignettes/images/general_figs/cortex_svz_location_fields.png
diff --git a/vignettes/images/general_figs/cyCIF_PDAC_image_summary.png b/vignettes/images/general_figs/cyCIF_PDAC_image_summary.png
diff --git a/vignettes/images/general_figs/cycif_paper_figure.png b/vignettes/images/general_figs/cycif_paper_figure.png
diff --git a/vignettes/images/general_figs/diagram_giotto_workflow.png b/vignettes/images/general_figs/diagram_giotto_workflow.png
diff --git a/vignettes/images/general_figs/merFISH_hypoth_image_summary.png b/vignettes/images/general_figs/merFISH_hypoth_image_summary.png
diff --git a/vignettes/images/general_figs/mouse_brain_highres.png b/vignettes/images/general_figs/mouse_brain_highres.png
diff --git a/vignettes/images/general_figs/mouse_kidney_highres.png b/vignettes/images/general_figs/mouse_kidney_highres.png
diff --git a/vignettes/images/general_figs/osmFISH_SS_cortex_image_summary.png b/vignettes/images/general_figs/osmFISH_SS_cortex_image_summary.png
diff --git a/vignettes/images/general_figs/osmfish_image_demo.png b/vignettes/images/general_figs/osmfish_image_demo.png
diff --git a/vignettes/images/general_figs/overview_datasets.png b/vignettes/images/general_figs/overview_datasets.png
diff --git a/vignettes/images/general_figs/overview_datasets2.png b/vignettes/images/general_figs/overview_datasets2.png
diff --git a/vignettes/images/general_figs/resolve_bioscience_cancer_summary.png b/vignettes/images/general_figs/resolve_bioscience_cancer_summary.png
diff --git a/vignettes/images/general_figs/starmap_cortex_image_summary.png b/vignettes/images/general_figs/starmap_cortex_image_summary.png
diff --git a/vignettes/images/general_figs/temp_workflow.png b/vignettes/images/general_figs/temp_workflow.png
diff --git a/vignettes/images/general_figs/visium_brain_image_summary.png b/vignettes/images/general_figs/visium_brain_image_summary.png
diff --git a/vignettes/images/general_figs/visium_kidney_image_summary.png b/vignettes/images/general_figs/visium_kidney_image_summary.png
diff --git a/vignettes/images/general_figs/visium_prostate_summary.png b/vignettes/images/general_figs/visium_prostate_summary.png
diff --git a/vignettes/images/general_figs/visium_technology.png b/vignettes/images/general_figs/visium_technology.png
diff --git a/vignettes/images/general_figs/vizgen_brain_summary.png b/vignettes/images/general_figs/vizgen_brain_summary.png
diff --git a/vignettes/images/seqscope_mouse_liver/HDMI_scatter.png b/vignettes/images/seqscope_mouse_liver/HDMI_scatter.png
diff --git a/vignettes/images/seqscope_mouse_liver/feature_distribution.png b/vignettes/images/seqscope_mouse_liver/feature_distribution.png
diff --git a/vignettes/images/seqscope_mouse_liver/leiden_spat.png b/vignettes/images/seqscope_mouse_liver/leiden_spat.png
diff --git a/vignettes/images/seqscope_mouse_liver/leiden_umap.png b/vignettes/images/seqscope_mouse_liver/leiden_umap.png
diff --git a/vignettes/images/seqscope_mouse_liver/polygon.png b/vignettes/images/seqscope_mouse_liver/polygon.png
diff --git a/vignettes/images/seqscope_mouse_liver/spatgenes.png b/vignettes/images/seqscope_mouse_liver/spatgenes.png
diff --git a/vignettes/images/seqscope_mouse_liver/top200.png b/vignettes/images/seqscope_mouse_liver/top200.png
diff --git a/vignettes/images/seqscope_mouse_liver/total_expr.png b/vignettes/images/seqscope_mouse_liver/total_expr.png
diff --git a/vignettes/images/singlecell_prostate_integration/4_cluster_with_integration.png b/vignettes/images/singlecell_prostate_integration/4_cluster_with_integration.png
diff --git a/vignettes/images/singlecell_prostate_integration/4_cluster_without_integration.png b/vignettes/images/singlecell_prostate_integration/4_cluster_without_integration.png
diff --git a/vignettes/images/singlecell_prostate_integration/4_list_with_integration.png b/vignettes/images/singlecell_prostate_integration/4_list_with_integration.png
diff --git a/vignettes/images/singlecell_prostate_integration/4_list_without_integration.png b/vignettes/images/singlecell_prostate_integration/4_list_without_integration.png
diff --git a/vignettes/images/singlecell_rna_seq/3_scree_plot.png b/vignettes/images/singlecell_rna_seq/3_scree_plot.png
diff --git a/vignettes/images/singlecell_rna_seq/4_Cluster.png b/vignettes/images/singlecell_rna_seq/4_Cluster.png
diff --git a/vignettes/images/singlecell_rna_seq/5_a_metaheatmap.png b/vignettes/images/singlecell_rna_seq/5_a_metaheatmap.png
diff --git a/vignettes/images/singlecell_rna_seq/5_b_violinplot_scran.png b/vignettes/images/singlecell_rna_seq/5_b_violinplot_scran.png
diff --git a/vignettes/images/singlecell_rna_seq/6_featureplot.png b/vignettes/images/singlecell_rna_seq/6_featureplot.png
diff --git a/vignettes/images/singlecell_rna_seq/7_Annotation.png b/vignettes/images/singlecell_rna_seq/7_Annotation.png
diff --git a/vignettes/images/singlecell_rna_seq/8_c_metaheatmap.png b/vignettes/images/singlecell_rna_seq/8_c_metaheatmap.png
diff --git a/vignettes/images/singlecell_rna_seq/8a_scree_plot.png b/vignettes/images/singlecell_rna_seq/8a_scree_plot.png
diff --git a/vignettes/images/singlecell_rna_seq/8b_Cluster.png b/vignettes/images/singlecell_rna_seq/8b_Cluster.png
diff --git a/vignettes/images/singlecell_rna_seq/8d_Annotation.png b/vignettes/images/singlecell_rna_seq/8d_Annotation.png
diff --git a/vignettes/images/stereoseq_mosta/1.png b/vignettes/images/stereoseq_mosta/1.png
diff --git a/vignettes/images/stereoseq_mosta/2.png b/vignettes/images/stereoseq_mosta/2.png
diff --git a/vignettes/images/stereoseq_mosta/3.png b/vignettes/images/stereoseq_mosta/3.png
diff --git a/vignettes/images/stereoseq_mosta/4.png b/vignettes/images/stereoseq_mosta/4.png
diff --git a/vignettes/images/stereoseq_mosta/5.png b/vignettes/images/stereoseq_mosta/5.png
diff --git a/vignettes/images/stereoseq_mosta/6.png b/vignettes/images/stereoseq_mosta/6.png
diff --git a/vignettes/images/stereoseq_mosta/7.png b/vignettes/images/stereoseq_mosta/7.png
diff --git a/vignettes/images/stereoseq_mosta/8.png b/vignettes/images/stereoseq_mosta/8.png
diff --git a/vignettes/images/stereoseq_mosta/9.png b/vignettes/images/stereoseq_mosta/9.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/1-spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/1-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/10-UMAP.png b/vignettes/images/visium_cytassist_human_glioblastoma/10-UMAP.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/11-rna_spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/11-rna_spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/12-protein_spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/12-protein_spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/13-UMAP.png b/vignettes/images/visium_cytassist_human_glioblastoma/13-UMAP.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/14-integrated_spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/14-integrated_spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/2-spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/2-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/3-spatPlot2D.png b/vignettes/images/visium_cytassist_human_glioblastoma/3-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/4-HVFplot.png b/vignettes/images/visium_cytassist_human_glioblastoma/4-HVFplot.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/5-screePlot.png b/vignettes/images/visium_cytassist_human_glioblastoma/5-screePlot.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/6-PCA.png b/vignettes/images/visium_cytassist_human_glioblastoma/6-PCA.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/7-screePlot.png b/vignettes/images/visium_cytassist_human_glioblastoma/7-screePlot.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/8-PCA.png b/vignettes/images/visium_cytassist_human_glioblastoma/8-PCA.png
diff --git a/vignettes/images/visium_cytassist_human_glioblastoma/9-UMAP.png b/vignettes/images/visium_cytassist_human_glioblastoma/9-UMAP.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/0-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/0-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/1-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/1-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/10-spatDimPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/10-spatDimPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/11-spatDimPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/11-spatDimPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/12-violinPlot.png b/vignettes/images/visium_cytassist_lungcancer/12-violinPlot.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/13-plotMetaDataHeatmap.png b/vignettes/images/visium_cytassist_lungcancer/13-plotMetaDataHeatmap.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/14-dimFeatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/14-dimFeatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/15-violinPlot.png b/vignettes/images/visium_cytassist_lungcancer/15-violinPlot.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/16-plotMetaDataHeatmap.png b/vignettes/images/visium_cytassist_lungcancer/16-plotMetaDataHeatmap.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/17-metaheatmap.png b/vignettes/images/visium_cytassist_lungcancer/17-metaheatmap.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/18-spatcellplot_1.png b/vignettes/images/visium_cytassist_lungcancer/18-spatcellplot_1.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/19-spatDimCellPlot.png b/vignettes/images/visium_cytassist_lungcancer/19-spatDimCellPlot.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/2-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/2-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/20-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/20-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/21-plotStatDelaunayNetwork.png b/vignettes/images/visium_cytassist_lungcancer/21-plotStatDelaunayNetwork.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/22-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/22-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/23-spatFeatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/23-spatFeatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/24-spatFeatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/24-spatFeatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/25-spatFeatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/25-spatFeatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/26-heatmap_correlated_genes.png b/vignettes/images/visium_cytassist_lungcancer/26-heatmap_correlated_genes.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/27-rank_correlated_groups.png b/vignettes/images/visium_cytassist_lungcancer/27-rank_correlated_groups.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/28-spatCellPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/28-spatCellPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/29-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/29-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/3-HVFplot.png b/vignettes/images/visium_cytassist_lungcancer/3-HVFplot.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/30-spatPlot2D.png b/vignettes/images/visium_cytassist_lungcancer/30-spatPlot2D.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/4-screePlot.png b/vignettes/images/visium_cytassist_lungcancer/4-screePlot.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/5-PCA.png b/vignettes/images/visium_cytassist_lungcancer/5-PCA.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/6-UMAP.png b/vignettes/images/visium_cytassist_lungcancer/6-UMAP.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/7-tSNE.png b/vignettes/images/visium_cytassist_lungcancer/7-tSNE.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/8-UMAP.png b/vignettes/images/visium_cytassist_lungcancer/8-UMAP.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/9-tSNE.png b/vignettes/images/visium_cytassist_lungcancer/9-tSNE.png
diff --git a/vignettes/images/visium_cytassist_lungcancer/CytAssist_Visium_workflow.png b/vignettes/images/visium_cytassist_lungcancer/CytAssist_Visium_workflow.png
diff --git a/vignettes/images/visium_mouse_brain/0-spatPlot2D.png b/vignettes/images/visium_mouse_brain/0-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/1-spatPlot2D.png b/vignettes/images/visium_mouse_brain/1-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/10-spatPlot2D.png b/vignettes/images/visium_mouse_brain/10-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/11-spatPlot2D.png b/vignettes/images/visium_mouse_brain/11-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/12-spatPlot2D.png b/vignettes/images/visium_mouse_brain/12-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/13-spatDimPlot2D.png b/vignettes/images/visium_mouse_brain/13-spatDimPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/14-violinPlot.png b/vignettes/images/visium_mouse_brain/14-violinPlot.png
diff --git a/vignettes/images/visium_mouse_brain/15-plotMetaDataHeatmap.png b/vignettes/images/visium_mouse_brain/15-plotMetaDataHeatmap.png
diff --git a/vignettes/images/visium_mouse_brain/16-dimFeatPlot2D.png b/vignettes/images/visium_mouse_brain/16-dimFeatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/17-violinPlot.png b/vignettes/images/visium_mouse_brain/17-violinPlot.png
diff --git a/vignettes/images/visium_mouse_brain/18-plotMetaDataHeatmap.png b/vignettes/images/visium_mouse_brain/18-plotMetaDataHeatmap.png
diff --git a/vignettes/images/visium_mouse_brain/19-dimFeatPlot2D.png b/vignettes/images/visium_mouse_brain/19-dimFeatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/2-HVFplot.png b/vignettes/images/visium_mouse_brain/2-HVFplot.png
diff --git a/vignettes/images/visium_mouse_brain/20-plotMetaDataCellsHeatmap.png b/vignettes/images/visium_mouse_brain/20-plotMetaDataCellsHeatmap.png
diff --git a/vignettes/images/visium_mouse_brain/21-spatCellPlot2D.png b/vignettes/images/visium_mouse_brain/21-spatCellPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/22-spatDimCellPlot2D.png b/vignettes/images/visium_mouse_brain/22-spatDimCellPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/23-spatCellPlot2D.png b/vignettes/images/visium_mouse_brain/23-spatCellPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/24-spatPlot2D.png b/vignettes/images/visium_mouse_brain/24-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/25-spatPlot2D.png b/vignettes/images/visium_mouse_brain/25-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/26-spatFeatPlot2D.png b/vignettes/images/visium_mouse_brain/26-spatFeatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/27-spatFeatPlot2D.png b/vignettes/images/visium_mouse_brain/27-spatFeatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/28-heatmSpatialCorFeats.png b/vignettes/images/visium_mouse_brain/28-heatmSpatialCorFeats.png
diff --git a/vignettes/images/visium_mouse_brain/29-rankSpatialCorGroups.png b/vignettes/images/visium_mouse_brain/29-rankSpatialCorGroups.png
diff --git a/vignettes/images/visium_mouse_brain/3-screePlot.png b/vignettes/images/visium_mouse_brain/3-screePlot.png
diff --git a/vignettes/images/visium_mouse_brain/30-spatCellPlot2D.png b/vignettes/images/visium_mouse_brain/30-spatCellPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/31-spatPlot2D.png b/vignettes/images/visium_mouse_brain/31-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/32-UMAP.png b/vignettes/images/visium_mouse_brain/32-UMAP.png
diff --git a/vignettes/images/visium_mouse_brain/33-spatPlot2D.png b/vignettes/images/visium_mouse_brain/33-spatPlot2D.png
diff --git a/vignettes/images/visium_mouse_brain/4-PCA.png b/vignettes/images/visium_mouse_brain/4-PCA.png
diff --git a/vignettes/images/visium_mouse_brain/5-UMAP.png b/vignettes/images/visium_mouse_brain/5-UMAP.png
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