increase legend text for cistrans plot and qtl histogram

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), 

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))