Figures valentina

figures/src/fig_rgi.R

+#!/usr/bin/Rscript
+
+## LOG FILE
+sink(file=file(snakemake@log[[1]], open="wt"), type="message")
+
+## NOTE
+# Plot RGI statistics
+
+## IMPORT
+suppressMessages(library(testit))
+suppressMessages(library(UpSetR))
+suppressMessages(library(ggplot2))
+suppressMessages(library(reshape2))
+# custom
+source(snakemake@params$utils)
+
+## DATA
+stats <- read.csv(
+    file=snakemake@input$stats,
+    sep="\t",
+    header=TRUE,
+    stringsAsFactors=FALSE,
+    check.names=FALSE
+)
+# reshape
+stats_melted <- reshape2::melt(stats, id.vars=c("label", "type"), variable.name="tool", value.name="count")
+# change names
+stats_melted$tool <- ASM_TOOL_NAMES[as.character(stats_melted$tool)]
+
+## PLOT
+plots <- list()
+for(dtype in unique(stats_melted$type)){
+    dtype_df <- stats_melted[stats_melted$type == dtype,]
+    plots[[dtype]] <-
+        ggplot(data=dtype_df, aes(x=tool, y=count, fill=tool)) +
+        geom_col() +
+        scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide="legend") +
+        facet_wrap(vars(label), ncol=round(sqrt(length(unique(dtype_df$label)))), scales="free_y") +
+        labs(
+            # title="",
+            # subtitle="",
+            x="",
+            y=RGI_NAMES$type[dtype]
+        ) +
+        theme_bw() +
+        theme(
+            # legend
+            legend.title=element_blank(),
+            # grid
+            panel.grid=element_blank(),
+            # strip
+            strip.background=element_rect(fill="white"),
+            strip.text=element_text(size=9, color="black"),
+            # axes
+            axis.title=element_text(size=12, color="black"),
+            axis.text.y=element_text(size=9, color="black"),
+            axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
+        )
+}
+# Total counts
+stats_melted_aro <- stats_melted[stats_melted$type == dtype,]
+stats_melted_aro <- aggregate(stats_melted_aro$count, by=list(tool=stats_melted_aro$tool), FUN=sum)
+plots[["total"]] <-
+    ggplot(data=stats_melted_aro, aes(x=tool, y=x, fill=tool)) +
+    geom_col() +
+    scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide="legend") +
+    labs(
+        # title="",
+        # subtitle="",
+        x="",
+        y="Total hits"
+    ) +
+    theme_bw() +
+    theme(
+        # legend
+        legend.title=element_blank(),
+        # grid
+        panel.grid=element_blank(),
+        # strip
+        strip.background=element_rect(fill="white"),
+        strip.text=element_text(size=9, color="black"),
+        # axes
+        axis.title=element_text(size=12, color="black"),
+        axis.text.y=element_text(size=9, color="black"),
+        axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
+    )
+
+## PDF
+pdf(snakemake@output$pdf, width=snakemake@params$width, height=snakemake@params$height)
+for(pp in plots){ print(pp) }
+dev.off()