From b1772973a4b9c9b1058d580329915735f7521f11 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Thu, 26 Jan 2017 18:58:06 -0500
Subject: [PATCH] ENH: Optimize plots for publication

Also refactor ggsave() export to multiple formats.
---
 .gitignore |  1 +
 plots.R    | 21 +++++++++++++--------
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index be049ac..b326ec5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,7 @@ z_stack/
 *.csv
 *.pdf
 *.png
+*.svg
 
 # Log files from CellProfiler Analyst
 *.log
diff --git a/plots.R b/plots.R
index 536a1c0..2635491 100644
--- a/plots.R
+++ b/plots.R
@@ -11,14 +11,21 @@ binwidth <- 0.025
 ## Bring RNAi to the front of the level list.
 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 = "."),
+                     ggplot2::ggsave, width = 8, height = 5,
+                     units = "in"))
+}
+
 ggplot(filter(wells_all, type == "RNAi"),
        aes(coloc, fill = significant)) +
     geom_histogram(binwidth = binwidth) +
-    scale_fill_manual(values = c("grey70", "blue")) +
-    ggtitle("Histogram of RNAi wells with significant overlap (p-value < 5%)") +
+    scale_fill_manual(values = c("grey", "blue")) +
+    ggtitle("Histogram of wells with significant overlap (p-value < 5%)") +
     xlab("% colocalization")
-ggsave("rnai-hist-signif.png")
-ggsave("rnai-hist-signif.pdf")
+plot_save("rnai-hist-signif")
 
 ggplot(wells_all, aes(coloc, color = type)) +
     geom_freqpoly(binwidth = binwidth) +
@@ -26,13 +33,11 @@ ggplot(wells_all, aes(coloc, color = type)) +
     facet_wrap(~ type) +
     ggtitle("Histogram of all well types") +
     xlab("% colocalization")
-ggsave("all-hist.png")
-ggsave("all-hist.pdf")
+plot_save("all-hist")
 
 ggplot(wells_all, aes(coloc, color = type)) +
     geom_density() +
     facet_wrap(~ type) +
     ggtitle("Density plot of wells to show distribution") +
     xlab("% colocalization")
-ggsave("all-density.png")
-ggsave("all-density.pdf")
+plot_save("all-density")