OncoPrint figures (#1200)

* Initial pass at histology palette overhaul * Add display columns for legends * Remove histology label palette NB from CI * Add broad histology order * Add oncoprint_include * Add oncoprint grouping info to palette df * Make cancer_group other darker; rerun * Pretty sure change in #1161 was unintentional * We have been manually editing the oncoprint palette I see * Remove/move/rename to prep for an oncoprint fig2 * Missed the instance where I recode based on other hex code * Rerun oncoprint now that palette is fixed * Change up approach to oncoprint * Remove oncoprint script that assembled from PNGs * Remove oncoprint PNGs * Add new oncoprint figure script saves individual panels as PDFs, also uses new palette * Add PDFs of oncoprints and legends * Add PDF draft of assembled figure 2 * Update figure shell script * Add fig 2 README * Add PNG version of draft figure 2 * Tweak the cancer group palette * Reorder HGAT legend; rerun with new palette * Remove outdated assembled figure * Add compiled versions Sizing and spacing probably still need work! * Update oncoprint palette * Rerun module with new palette * Rerun pub ready figure versions of oncoprints * Add complex event to oncoprint palette * Rerun module with complex event in palette * Rerun oncoprint fig script with complex events * Darker complex event hex code * Try a "wine" color for complex event * Remove outdated PNG & PDF of compiled fig * Update figures/generate-figures.sh Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
AlexsLemonade · Jan 4, 2022 · ddb6a8c · ddb6a8c
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diff --git a/analyses/oncoprint-landscape/plots/primary-plus_embryonal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_embryonal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_embryonal_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_embryonal_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_hgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_hgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_hgat_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_hgat_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_lgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_lgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_lgat_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_lgat_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_other_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_other_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_other_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_other_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_embryonal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_embryonal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_embryonal_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_embryonal_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_hgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_hgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_hgat_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_hgat_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_lgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_lgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_lgat_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_lgat_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_other_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_other_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_other_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_other_oncoprint.png
diff --git a/figures/generate-figures.sh b/figures/generate-figures.sh
@@ -32,6 +32,11 @@ mkdir -p pdfs
 Rscript --vanilla scripts/color_palettes.R
 Rscript -e "rmarkdown::render('mapping-histology-labels.Rmd', clean = TRUE)"
 
+################ Sample distribution
+# Run sample distribution analysis
+bash ${analyses_dir}/sample-distribution-analysis/run-sample-distribution.sh
+
+# TODO: Rscript for figure (related: https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1175)
 
 ######################
 ## Interaction plots
@@ -77,14 +82,8 @@ bash ${analyses_dir}/oncoprint-landscape/run-oncoprint.sh
 # Will create two plots - primary only and "primary plus" samples
 filenames=(primary_only primary-plus)
 
-for filename in "${filenames[@]}"; do
-
-  ## Run the `oncoprint-landscape` figure assembly script
-  Rscript --vanilla scripts/oncoprint-landscape.R \
-    --lead_filename ${filename} \
-    --png_name pngs/${filename}_oncoprint_landscape.png
-
-done
+# Create single panel PDFs and legends
+Rscript --vanilla scripts/fig2-oncoprint-landscape.R
 
 ####### Telomerase Activities
 

diff --git a/figures/palettes/oncoprint_color_palette.tsv b/figures/palettes/oncoprint_color_palette.tsv
@@ -11,11 +11,13 @@ In_Frame_Ins	#FFE4E1
 Stop_Codon_Ins	#CC79A7
 Start_Codon_Del	#56B4E9
 Fusion	#7B68EE
-Multi_Hit	#00F021
+Multi_Hit	#CCCCCC
 Hom_Deletion	#313695
 Hem_Deletion	#abd9e9
-amplification	#c51b7d
-loss	#0072B2
-gain	#D55E00
-High_Level_Gain	#FF0000
+Del	#386db0
+Amp	#c51b7d
 Multi_Hit_Fusion	#CD96CD
+Intron	#5ea4fe
+5'Flank	#7CCBAC
+3'Flank	#FD8344
+Complex_Event	#571242
diff --git a/figures/pdfs/fig2/README.md b/figures/pdfs/fig2/README.md
@@ -0,0 +1,6 @@
+### Figure 2
+
+Figure 2 is compiled from the output of `figures/scripts/fig2-oncoprint-landscape.R`
+
+The individual panels and legends can be found in `panels`.
+They are compiled via Adobe Illustrator, saved as a PDF to this directory, and then a PNG file is exported to `figures/pngs`.
diff --git a/figures/pdfs/fig2/panels/embryonal_oncoprint_cancer_group_legend.pdf b/figures/pdfs/fig2/panels/embryonal_oncoprint_cancer_group_legend.pdf
diff --git a/figures/pdfs/fig2/panels/germline_sex_legend.pdf b/figures/pdfs/fig2/panels/germline_sex_legend.pdf
diff --git a/figures/pdfs/fig2/panels/hgat_oncoprint_cancer_group_legend.pdf b/figures/pdfs/fig2/panels/hgat_oncoprint_cancer_group_legend.pdf
diff --git a/figures/pdfs/fig2/panels/lgat_oncoprint_cancer_group_legend.pdf b/figures/pdfs/fig2/panels/lgat_oncoprint_cancer_group_legend.pdf
diff --git a/figures/pdfs/fig2/panels/oncoprint_alteration_legend.pdf b/figures/pdfs/fig2/panels/oncoprint_alteration_legend.pdf
diff --git a/figures/pdfs/fig2/panels/other_oncoprint_cancer_group_legend.pdf b/figures/pdfs/fig2/panels/other_oncoprint_cancer_group_legend.pdf
diff --git a/figures/pdfs/fig2/panels/primary_only_embryonal_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_only_embryonal_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_only_hgat_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_only_hgat_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_only_lgat_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_only_lgat_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_only_other_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_only_other_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_plus_embryonal_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_plus_embryonal_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_plus_hgat_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_plus_hgat_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_plus_lgat_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_plus_lgat_oncoprint.pdf
diff --git a/figures/pdfs/fig2/panels/primary_plus_other_oncoprint.pdf b/figures/pdfs/fig2/panels/primary_plus_other_oncoprint.pdf
diff --git a/figures/pdfs/supp/primary_only_other_supplemental_oncoprint.pdf b/figures/pdfs/supp/primary_only_other_supplemental_oncoprint.pdf
diff --git a/figures/pdfs/supp/primary_plus_other_supplemental_oncoprint.pdf b/figures/pdfs/supp/primary_plus_other_supplemental_oncoprint.pdf
diff --git a/figures/pngs/fig1-openpbta-distribution.png b/figures/pngs/fig1-openpbta-distribution.png
diff --git a/figures/pngs/fig2-mutational-landscapes.png b/figures/pngs/fig2-mutational-landscapes.png
diff --git a/figures/pngs/primary-plus_oncoprint_landscape.png b/figures/pngs/primary-plus_oncoprint_landscape.png
diff --git a/figures/pngs/primary_only_oncoprint_landscape.png b/figures/pngs/primary_only_oncoprint_landscape.png
diff --git a/figures/scripts/color_palettes.R b/figures/scripts/color_palettes.R
@@ -97,7 +97,7 @@ divergent_df <- data.frame(color_names = divergent_color_names,
 # col_fun <- circlize::colorRamp2(divergent_col_val,
 #                                 divergent_col_palette)
 
-### 4) A binary color key which are the most extreme colors in the divergent color scale. 
+### 4) A binary color key which are the most extreme colors in the divergent color scale.
 binary_col_palette <- c("#2166ac",
                         "#b2182b",
                          na_color)
@@ -124,14 +124,16 @@ oncoprint_col_palette <- c("#35978f",
                            "#CC79A7",
                            "#56B4E9",
                            "#7B68EE",
-                           "#00F021",
+                           "#CCCCCC",
                            "#313695",
                            "#abd9e9",
+                           "#386db0",
                            "#c51b7d",
-                           "#0072B2",
-                           "#D55E00",
-                           "#FF0000",
-                           "#CD96CD")
+                           "#CD96CD",
+                           "#5ea4fe",
+                           "#7CCBAC",
+                           "#FD8344",
+                           "#571242")
 
 oncoprint_color_names <- c("Missense_Mutation",
                            "Nonsense_Mutation",
@@ -148,11 +150,13 @@ oncoprint_color_names <- c("Missense_Mutation",
                            "Multi_Hit",
                            "Hom_Deletion",
                            "Hem_Deletion",
-                           "amplification",
-                           "loss",
-                           "gain",
-                           "High_Level_Gain",
-                           "Multi_Hit_Fusion")
+                           "Del",
+                           "Amp",
+                           "Multi_Hit_Fusion",
+                           "Intron",
+                           "5'Flank",
+                           "3'Flank",
+                           "Complex_Event")
 
 # Format as data.frame
 oncoprint_df <- data.frame(color_names = oncoprint_color_names,
@@ -179,7 +183,7 @@ oncoprint_df <- data.frame(color_names = oncoprint_color_names,
   # Cat this out
   cat(swatches)
  }
- 
+
  # Format as data.frame
  tumor_descriptor_palette <- data.frame(color_names = c("Initial CNS Tumor",
                                                         "Progressive",
@@ -192,7 +196,7 @@ oncoprint_df <- data.frame(color_names = oncoprint_color_names,
                                                       "#FD8CC1FF",
                                                       "#FD7446FF")) %>%
    readr::write_tsv(file.path(output_dir, "tumor_descriptor_palette.tsv"))
- 
+
 #
 # Usage:
 # Put whichever color palette you are updating into function.

diff --git a/figures/scripts/fig2-mutational-landscape.R → ...scripts/deprecated/mutational-landscape.R b/figures/scripts/fig2-mutational-landscape.R → ...scripts/deprecated/mutational-landscape.R