Figures valentina

figures/src/fig_partial_genes.R

+#!/usr/bin/Rscript
+
+## LOG FILE
+sink(file=file(snakemake@log[[1]], open="wt"), type="message")
+
+## NOTE
+# Plot protein/gene counts
+
+## IMPORT
+suppressMessages(library(testit))
+suppressMessages(library(ggplot2))
+suppressMessages(library(reshape2))
+# custom
+source(snakemake@params$utils)
+
+## DATA
+counts <- read.csv(
+    file=snakemake@input$counts,
+    sep="\t",
+    header=TRUE,
+    stringsAsFactors=FALSE,
+    check.names=FALSE
+)
+# change tool names
+counts$tool <- GENE_TOOL_NAMES[counts$tool]
+colnames(counts) <- sapply(colnames(counts), function(x){ ifelse(x %in% names(ASM_TOOL_NAMES), ASM_TOOL_NAMES[x], x) })
+# reshape
+counts_melted <- reshape2::melt(counts, id.vars="tool")
+# Gene tool name - as ordered factor
+counts_melted$tool <- factor(counts_melted$tool, levels=GENE_TOOL_NAMES, ordered=TRUE)
+# Gene tool name - short version
+counts_melted$tool_name <- sapply(as.character(counts_melted$tool), function(x){ unlist(strsplit(x, " "))[1] })
+
+## PLOT
+counts_p <-
+    ggplot(data=counts_melted, aes(x=tool, y=value, fill=variable)) +
+    geom_col(position = "dodge") +
+    scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide="legend") +
+    facet_wrap(vars(tool_name), nrow=1, scales="free_x") +
+    labs(
+        # title="",
+        # subtitle="",
+        x="",
+        y="Number of proteins/genes"
+    ) +
+    theme_bw() +
+    theme(
+        # legend
+        legend.title=element_blank(),
+        # grid
+        panel.grid=element_blank(),
+        # strip
+        strip.background=element_rect(fill="white"),
+        strip.text=element_text(size=12, color="black"),
+        # axes
+        axis.title=element_text(size=12, color="black"),
+        axis.text.y=element_text(size=9, color="black"),
+        axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
+    )
+
+## PDF
+pdf(snakemake@output$pdf, width=snakemake@params$width, height=snakemake@params$height)
+print(counts_p)
+dev.off()