Initial commit

Author: niekwit

workflow/scripts/plot_frip.R

@@ -0,0 +1,54 @@
+# Redirect R output to log
+log <- file(snakemake@log[[1]], open = "wt")
+sink(log, type = "output")
+sink(log, type = "message")
+
+library(tidyverse)
+library(cowplot)
+
+# Plot bar graph of FRiP values
+total_read_counts <- snakemake@input[["total_read_counts"]]
+peak_read_counts <- snakemake@input[["peak_read_count"]]
+
+# df to store FRiP values
+df <- data.frame(sample = character(),
+                 read_in_peaks = numeric(),
+                 total_reads = numeric(),
+                 fraction_of_reads_in_peaks = numeric())
+
+# Add FRiP values to df
+for (i in seq_along(total_read_counts)) {
+  sample <- snakemake@wildcards[["bg_sample"]][i]
+  total_reads <- as.numeric(read_lines(total_read_counts[i]))
+  peak_reads <- as.numeric(read_lines(peak_read_counts[i]))
+  frip <- peak_reads / total_reads
+  
+  df <- df %>%
+    add_row(sample = sample,
+            read_in_peaks = peak_reads,
+            total_reads = total_reads,
+            fraction_of_reads_in_peaks = frip)
+}
+
+# Create plot
+p <- ggplot(df, aes(x = sample, 
+                    y = fraction_of_reads_in_peaks)) +
+  geom_bar(stat = "identity", 
+           fill = "#419179",
+           colour = "black") +
+  theme_cowplot(18) +
+  theme(axis.text.x = element_text(angle = 45, 
+                                   hjust = 1)) +
+  scale_y_continuous(expand = expansion(mult = c(0, 0.1)),
+                     limits = c(0, 1)) +
+  labs(title = NULL,
+       x = NULL,
+       y = "Fraction of reads in peaks") +
+  theme(plot.title = element_text(hjust = 0.5))
+
+# Save plot
+ggsave(snakemake@output[[1]], p)
+
+# Close redirection of output/messages
+sink(log, type = "output")
+sink(log, type = "message")