From 1223305a79bf2267ae7c3171229b4a95f3031d4f Mon Sep 17 00:00:00 2001
From: "Hartanto, Margi" <margi.hartanto@wur.nl>
Date: Tue, 18 Feb 2020 18:36:15 +0100
Subject: [PATCH] increase legend text for cistrans plot and qtl histogram
---
3-eqtl-visualization.R | 18 +++++++++++-------
4-qtl-integration.R | 10 ++++++----
2 files changed, 17 insertions(+), 11 deletions(-)
diff --git a/3-eqtl-visualization.R b/3-eqtl-visualization.R
index c5184e3..cf86a1d 100644
--- a/3-eqtl-visualization.R
+++ b/3-eqtl-visualization.R
@@ -299,14 +299,16 @@
eqtl.plot <- ggplot(all.eqtl.table3, aes(x = qtl_bp, y = gene_bp)) +
geom_segment(aes(x = qtl_bp_left, y = gene_bp, xend = qtl_bp_right, yend = gene_bp),
alpha = 0.75, colour = "grey") +
- geom_point(aes(colour = ordered(stage, levels = c("local\neQTL", "pd", "ar", "im", "rp")),
- shape = allele,
- size = abs(qtl_effect),
- alpha = log10(qtl_significance))
- ) +
- scale_alpha(range = c(0.3, 1)) +
+ geom_point(aes(colour = ordered(stage, levels = c("local\neQTL", "pd", "ar", "im", "rp"))
+ #, shape = allele,
+ #size = abs(qtl_effect),
+ #alpha = log10(qtl_significance))
+ )) +
+ #scale_alpha(range = c(0.3, 1)) +
facet_grid(fct_rev(gene_chromosome) ~ qtl_chromosome, space = "free", scales = "free") +
presentation +
+ theme(legend.title= element_text(size = 12, face = "bold"),
+ legend.text = element_text(size = 12)) +
scale_colour_manual('stage', values = c('black','#ccbb44', '#228833', '#4477aa', '#cc3311')) +
labs(x = "eQTL peak position (Mb)", y = "Gene position (Mb)") +
scale_x_continuous(breaks=c(5, 10, 15, 20, 25, 30, 35, 40)*10^6,labels=c(5, 10, 15, 20, 25, 30, 35, 40)) +
@@ -335,7 +337,9 @@
facet_grid(factor(stage, levels = c("pd", "ar", "im", "rp")) ~ qtl_chromosome, space = "free",scales="free") +
presentation +
scale_fill_manual('stage', values = c('#ccbb44', '#228833', '#4477aa', '#cc3311')) +
- theme(legend.position = "right", legend.text=element_text(size=10)) +
+ theme(legend.position = "right",
+ legend.text = element_text(size = 12),
+ legend.title = element_text(size = 12, face = 'bold')) +
labs(x="eQTL peak position (Mb)",y="eQTL counts") +
ylim(c(0, 100)) +
geom_hline(data = hist.threshold, aes(yintercept = threshold),
diff --git a/4-qtl-integration.R b/4-qtl-integration.R
index e391455..f7b73e3 100644
--- a/4-qtl-integration.R
+++ b/4-qtl-integration.R
@@ -49,7 +49,7 @@
# creating the histogram plot ####
# plot style ####
- presentation <- theme(axis.text.x = element_text(size=12, face="bold", color="black"),
+ presentation <- theme(axis.text.x = element_text(size=10, face="bold", color="black"),
axis.text.y = element_text(size=12, face="bold", color="black"),
axis.title.x = element_text(size=15, face="bold", color="black"),
axis.title.y = element_text(size=15, face="bold", color="black"),
@@ -59,7 +59,9 @@
panel.background = element_rect(fill = "white",color="black"),
panel.grid.major = element_line(colour = "grey80"),
panel.grid.minor = element_blank(),
- legend.position = "right")
+ legend.position = "right",
+ legend.title = element_text(size = 12, face = 'bold'),
+ legend.text = element_text(size = 12))
myColors <- brewer.pal(9,"Set1")[c(3,5,9,6,7)]
myColors <- c("black",brewer.pal(9,"Set1")[c(2,9)])
@@ -91,8 +93,8 @@
#geom_density(alpha = 0.5) +
facet_grid(factor(qtl_level, level = c('phQTL', 'mQTL', 'eQTL')) ~ qtl_chromosome, scales="free_y") +
presentation +
- scale_fill_manual(values = c('#964B00', '#ccbb44', '#228833', '#4477aa', '#cc3311')) +
- theme(legend.position = "top", legend.text=element_text(size=5)) +
+ scale_fill_manual(values = c('#000000', '#ccbb44', '#228833', '#4477aa', '#cc3311')) +
+ theme(legend.position = "top") +
labs(x="QTL peak position (Mb)",y="QTL counts") +
scale_x_continuous(breaks=c(5, 10, 15, 20, 25, 30, 35, 40)*10^6,labels=c(5, 10, 15, 20, 25, 30, 35, 40))
--
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