From e5d2dac19958dab4d0a785037a659ff806ad54c1 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Tue, 7 Feb 2017 12:16:10 -0500
Subject: [PATCH] ENH: Add histogram plot for significant genes

- Add prefix to plot output
---
 plots.R | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/plots.R b/plots.R
index 2635491..bcda9ba 100644
--- a/plots.R
+++ b/plots.R
@@ -13,8 +13,9 @@ wells_all$type <- relevel(wells_all$type, "RNAi")
 
 theme_set(theme_bw())
 
-plot_save <- function(prefix, extensions = c("png", "pdf", "svg")) {
-    invisible(sapply(paste(prefix, extensions, sep = "."),
+plot_save <- function(prefix, dir = "plots",
+                      extensions = c("png", "pdf", "svg")) {
+    invisible(sapply(file.path(dir, paste(prefix, extensions, sep = ".")),
                      ggplot2::ggsave, width = 8, height = 5,
                      units = "in"))
 }
@@ -23,10 +24,21 @@ ggplot(filter(wells_all, type == "RNAi"),
        aes(coloc, fill = significant)) +
     geom_histogram(binwidth = binwidth) +
     scale_fill_manual(values = c("grey", "blue")) +
-    ggtitle("Histogram of wells with significant overlap (p-value < 5%)") +
+    ggtitle("Histogram of RNAi wells with significant overlap (p-value < 5%)") +
     xlab("% colocalization")
 plot_save("rnai-hist-signif")
 
+ggplot(filter(wells_all,
+              !is.na(control),
+              plate == "160415_015529-V"),
+       aes(coloc, fill = significant)) +
+    geom_histogram(binwidth = binwidth) +
+    facet_wrap(~ control) +
+    scale_fill_manual(values = c("grey", "blue")) +
+    ggtitle(paste("Histogram of control wells with",
+                  "significant overlap (p-value < 5%)")) +
+    xlab("% colocalization")
+
 ggplot(wells_all, aes(coloc, color = type)) +
     geom_freqpoly(binwidth = binwidth) +
     scale_y_log10() +