Figures valentina

figures/src/mmseq_upsetr.R

+#!/usr/bin/Rscript
+
+## LOG FILE
+sink(file=file(snakemake@log[[1]], open="wt"), type="message")
+
+## NOTE
+# UpSetR
+# https://cran.r-project.org/web/packages/UpSetR/vignettes/basic.usage.html
+
+## IMPORT
+suppressMessages(library(testit))
+suppressMessages(library(UpSetR))
+# custom
+source(snakemake@params$utils)
+
+## DATA
+# overlap/intersection sizes
+overlap_sizes <- read.csv(
+    file=snakemake@input$overlap_sizes,
+    sep=" ",
+    header=FALSE,
+    stringsAsFactors=FALSE
+)
+# check: all expected tools are there
+testit::assert(all(sapply(names(TOOL_NAMES), function(x){ x %in% overlap_sizes$V2 })))
+# process names
+for(tname in names(TOOL_NAMES)){
+    overlap_sizes$V2 <- sub(tname, TOOL_NAMES[tname], overlap_sizes$V2)
+}
+overlap_sizes$V2 <- gsub("_", "&", overlap_sizes$V2)
+# create input for UpSetR
+overlap_names <- overlap_sizes$V2
+overlap_sizes <- overlap_sizes$V1
+names(overlap_sizes) <- overlap_names
+
+## PLOT
+pdf(snakemake@output$pdf, width=snakemake@params$width, height=snakemake@params$height)
+UpSetR::upset(
+    data=UpSetR::fromExpression(overlap_sizes),
+    # overlap order
+    order.by="degree",
+    decreasing=FALSE,
+    # colors
+    # queries=lapply(
+    #     TOOL_NAMES,
+    #     function(x){ list(query=UpSetR::intersects, params=list(x), color=TOOL_COLORS$proc[[x]], active=TRUE) }
+    # ),
+    set.metadata=list(
+        data=data.frame(
+            sets=TOOL_NAMES,
+            Tool=TOOL_NAMES,
+            stringsAsFactors=FALSE
+        ), 
+        plots=list(list(type="matrix_rows", column="Tool", colors=TOOL_COLORS$proc, alpha=0.7))
+    )
+)
+dev.off()