Figures valentina

figures/src/fig_rgi.R

@@ -23,51 +23,12 @@ stats <- read.csv(
     check.names=FALSE
 )
 # reshape
-stats_melted <- reshape2::melt(stats, id.vars=c("label", "type"), variable.name="tool", value.name="count")
+stats_melted <- reshape2::melt(stats, id.vars=c("label", "col", "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$notmeth, guide=NULL) +
-        facet_wrap(vars(label), ncol=round(sqrt(length(unique(dtype_df$label)))), scales="free_y") +
-        labs(
-            # title="",
-            # subtitle="",
-            x="",
-            y=RGI_NAMES$type[dtype]
-        ) +
-        theme_bw() +
-        theme(
-            # grid
-            panel.grid=element_blank(),
-            # strip
-            strip.background=element_rect(fill="white"),
-            strip.text=element_text(size=9, color="black"),
-            # axes
-            axis.title=element_text(size=12, color="black"),
-            axis.text.y=element_text(size=9, color="black"),
-            axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
-        )
-}
-# Total counts
-stats_melted_aro <- stats_melted[stats_melted$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=NULL) +
-    labs(
-        # title="",
-        # subtitle="",
-        x="",
-        y="Total hits"
-    ) +
+my_theme <- 
     theme_bw() +
     theme(
         # grid
@@ -81,6 +42,53 @@ plots[["total"]] <-
         axis.text.x=element_text(size=9, color="black", angle=90, vjust=0.5, hjust=1)
     )
 
+plots <- list()
+for(ctype in unique(stats_melted$type)){
+    # Counts per feature type
+    for(col in unique(stats_melted$col)){
+        df <- stats_melted[stats_melted$type == ctype & stats_melted$col == col,]
+        plots[[sprintf("%s_%s", ctype, col)]] <-
+            ggplot(data=df, aes(x=tool, y=count, fill=tool)) +
+            geom_col() +
+            scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide=NULL) +
+            facet_wrap(vars(label), ncol=round(sqrt(length(unique(df$label)))), scales="free_y") +
+            labs(
+                # title="",
+                subtitle=sprintf("Hits: %s", ctype),
+                x="",
+                y=RGI_NAMES$col[col]
+            ) +
+            my_theme
+    }
+    # Total counts
+    # df <- stats_melted[stats_melted$type == ctype,]
+    # df <- aggregate(df$count, by=list(tool=df$tool), FUN=sum)
+    # plots[[sprintf("%s_%s", ctype, "total")]] <-
+    #     ggplot(data=df, aes(x=tool, y=x, fill=tool)) +
+    #     geom_col() +
+    #     scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide=NULL) +
+    #     labs(
+    #         # title="",
+    #         subtitle=sprintf("Hits: %s", ctype),
+    #         x="",
+    #         y="Total hits"
+    #     ) +
+    #     my_theme
+}
+# Total counts
+df <- stats_melted[stats_melted$col == "ARO",]
+df <- aggregate(df$count, by=list(tool=df$tool, type=df$type), FUN=sum)
+plots[[sprintf("%s_%s", ctype, "total")]] <-
+    ggplot(data=df, aes(x=tool, y=x, fill=tool)) +
+    geom_col() +
+    scale_fill_manual(values=ASM_TOOL_COLORS$notmeth, guide=NULL) +
+    facet_wrap(vars(type), ncol=3) +
+    labs(
+        x="",
+        y="Total hits"
+    ) +
+    my_theme
+
 ## PDF
 pdf(snakemake@output$pdf, width=snakemake@params$width, height=snakemake@params$height)
 for(pp in plots){ print(pp) }