Combine broad histology oncoprints into a single multi-panel plot (Al…

…exsLemonade#1051)

* add multi panel png for histology specific oncoprints

* label individual oncoprints

- create loop in generate figures script to run `oncoprint-landscape.R` for each set of samples (primary_only and primary-plus)
- remove previous figures

* accommodate for the GOI list revisions made in AlexsLemonade#1053

* redesign `oncoprint-landscape.R`

* remove unnecessary files

- fix spacing in shell script

* actually fix spacing in shell script

* replace `transcriptomic_figure` with more accurate `oncoprint_figure`

Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>

figures/generate-figures.sh

@@ -77,8 +77,17 @@ fi
 # Run the `oncoprint-landscape` module shell script
 bash ${analyses_dir}/oncoprint-landscape/run-oncoprint.sh
 
-# Copy the primary plus samples oncoprint figure to final directory
-cp ${analyses_dir}/oncoprint-landscape/plots/all_participants_primary-plus_goi_oncoprint.png pngs/fig3-oncoprint-landscape.png
+# Will create two plots - primary only and "primary plus" samples
+filenames=(primary_only primary-plus)
+
+for filename in "${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
 
 ## Copy number status heatmap
 

figures/scripts/oncoprint-landscape.R

@@ -0,0 +1,106 @@
+# Chante Bethell for ALSF CCDL 2021
+#
+# Makes a multipanel plot for broad histology specific oncoprints.
+#
+# Code for this script was adapted from 
+# `figures/scripts/transcriptomic-overview.R`
+
+#### Set Up --------------------------------------------------------------------
+
+# Load maftools
+library(maftools)
+
+# Load multipanelfigure for figure assembly later
+library(multipanelfigure)
+
+# Get `magrittr` pipe
+`%>%` <- dplyr::`%>%`
+
+#### Directories and Files -----------------------------------------------------
+
+# Detect the ".git" folder -- this will in the project root directory.
+# Use this as the root directory to ensure proper execution, no matter where
+# it is called from.
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Declare output directory
+output_dir <- file.path(root_dir, "figures", "pngs")
+
+# Oncoprint directory
+onco_dir <- file.path(root_dir, "analyses", "oncoprint-landscape", "plots")
+
+#### Command line options ------------------------------------------------------
+
+# Declare command line options
+option_list <- list(
+  optparse::make_option(
+    c("-l", "--lead_filename"),
+    type = "character",
+    default = NULL,
+    help = "the leading filename for the oncoprints -- can be primary_only or primary-plus"
+  ),
+  optparse::make_option(
+    c("-p", "--png_name"),
+    type = "character",
+    default = NULL,
+    help = "oncoprint output png file name"
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+#### PNG names ----------------------------------------------------------------
+
+# Here we'll set up the file names for the broad histology specific oncoprints
+# stored in the `oncoprint-landscape` module
+lgat_png <- file.path(onco_dir, paste0(opt$lead_filename, "_lgat_goi_oncoprint.png"))
+embryonal_png <- file.path(onco_dir, paste0(opt$lead_filename, "_embryonal_goi_oncoprint.png"))
+hgat_png <- file.path(onco_dir, paste0(opt$lead_filename, "_hgat_goi_oncoprint.png"))
+ependymal_png <- file.path(onco_dir, paste0(opt$lead_filename, "_ependymal_goi_oncoprint.png"))
+other_cns_png <- file.path(onco_dir, paste0(opt$lead_filename, "_other_goi_oncoprint.png"))
+
+#### Assemble multipanel figure ------------------------------------------------
+
+oncoprint_figure <- multi_panel_figure(columns = 8,
+                                            rows = 2,
+                                            width = 1200,
+                                            height = 300)
+
+oncoprint_figure <- fill_panel(oncoprint_figure,
+                                    lgat_png,
+                                    col = 2:3,
+                                    row = 1,
+                                    scaling = "stretch",
+                                    label = "Low-grade astrocytic tumor")
+
+oncoprint_figure <- fill_panel(oncoprint_figure,
+                                    embryonal_png,
+                                    col = 4:5,
+                                    row = 1,
+                                    scaling = "stretch",
+                                    label = "Embryonal tumor")
+
+oncoprint_figure <- fill_panel(oncoprint_figure,
+                                    hgat_png,
+                                    col = 6:7,
+                                    row = 1,
+                                    scaling = "stretch",
+                                    label = "Diffuse astrocytic and oligodendroglial tumor")
+
+oncoprint_figure <- fill_panel(oncoprint_figure,
+                                    ependymal_png,
+                                    col = 2:3,
+                                    row = 2,
+                                    scaling = "stretch",
+                                    label = "Ependymal tumor")
+
+oncoprint_figure <- fill_panel(oncoprint_figure,
+                                    other_cns_png,
+                                    col = 4:5,
+                                    row = 2,
+                                    scaling = "stretch",
+                                    label = "Other CNS")
+
+save_multi_panel_figure(oncoprint_figure, opt$png_name)