fix x axis on integrated qtl figure

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") +

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