From 07c1b041b5ac960b357d52e65bd03daed1d4fcfe Mon Sep 17 00:00:00 2001
From: "Hartanto, Margi" <margi.hartanto@wur.nl>
Date: Thu, 16 Apr 2020 20:56:33 +0200
Subject: [PATCH] fix x axis on integrated qtl figure
---
4-qtl-integration.R | 3 ++-
5-create-community-network.R | 1 +
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/4-qtl-integration.R b/4-qtl-integration.R
index f7b73e3..8a906c7 100644
--- a/4-qtl-integration.R
+++ b/4-qtl-integration.R
@@ -91,7 +91,8 @@
qtl.hist <- ggplot(all.peak, aes(x=qtl_bp, fill = stage)) +
geom_histogram(binwidth = 2000000, right = T, origin = 0, alpha = 1) +
#geom_density(alpha = 0.5) +
- facet_grid(factor(qtl_level, level = c('phQTL', 'mQTL', 'eQTL')) ~ qtl_chromosome, scales="free_y") +
+ facet_grid(factor(qtl_level, level = c('phQTL', 'mQTL', 'eQTL')) ~ qtl_chromosome, scales="free") +
+
presentation +
scale_fill_manual(values = c('#000000', '#ccbb44', '#228833', '#4477aa', '#cc3311')) +
theme(legend.position = "top") +
diff --git a/5-create-community-network.R b/5-create-community-network.R
index e0e1ebc..277d040 100644
--- a/5-create-community-network.R
+++ b/5-create-community-network.R
@@ -314,6 +314,7 @@
mean = round(apply(degree.table[2:ncol(degree.table)], 1, mean), 2),
sd = round(apply(degree.table[2:ncol(degree.table)], 1, sd), 2))
all.rank <- all.rank[order(all.rank$mean), ]
+ write.csv(degree.table, paste0('networks/', dev.stage, chr, '-ranks-for-all-threshold.csv'))
write.csv(all.rank, paste0('networks/', dev.stage, chr, '-ranks.csv'))
# visualize the network
--
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