Figures valentina

figures/src/fig_crispr.R

+#!/usr/bin/Rscript
+
+## LOG FILE
+sink(file=file(snakemake@log[[1]], open="wt"), type="message")
+
+## NOTE
+# Plot CRISPR statistics
+
+## IMPORT
+suppressMessages(library(testit))
+suppressMessages(library(UpSetR))
+suppressMessages(library(ggplot2))
+# custom
+source(snakemake@params$utils)
+
+## DATA
+stats <- read.csv(
+    file=snakemake@input$stats,
+    sep="\t",
+    header=TRUE,
+    stringsAsFactors=FALSE,
+    check.names=FALSE
+)
+# change names
+stats$crispr_tool <- CRISPR_TOOL_NAMES[stats$crispr_tool]
+stats$asm_tool    <- ASM_TOOL_NAMES[stats$asm_tool]
+
+## PLOT: UpSetR + PDF
+plot_upsetr <- function(df, asm_tool){
+    asm_sets <- lapply(
+        CRISPR_TOOL_NAMES,
+        function(x){ unique(unlist(df[df$asm_tool==asm_tool & df$crispr_tool == x,"seq_id"])) }
+    )
+    names(asm_sets) <- CRISPR_TOOL_NAMES[names(asm_sets)]
+    UpSetR::upset(data=UpSetR::fromList(asm_sets), order.by="degree", decreasing=FALSE)
+}
+
+# NOTE:
+#   For an unknown reason creating and saving multiple plots using a for-loop or sapply did not work - the PDF was empty.
+#   Creating a PDF per plot in a for-loop or using sapply did not work either - each PDF was empty.
+pdf(snakemake@output$pdf, width=snakemake@params$width, height=snakemake@params$height)
+plot_upsetr(stats, "Flye")
+plot_upsetr(stats, "MEGAHIT")
+plot_upsetr(stats, "metaSPAdes")
+plot_upsetr(stats, "metaSPAdes (H)")
+dev.off()
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