cometics

dge_workflow/cuffdiff_report.R

@@ -202,11 +202,12 @@ fpkmSCVPlot(genes(cuff))
 #fpkmSCVPlot(genes(cuff), showPool=T)
 
 #' To assess the distributions of FPKM scores across samples, we plot their densities
-csDensity(genes(cuff))
+#csDensity(genes(cuff))
 #ggsave2(csBoxplot(genes(cuff))+ ggtitle("fpkm boxplots"))
 
-csDensity(genes(cuff),features=T)
+#csDensity(genes(cuff),features=T)
 csBoxplot(genes(cuff),replicates=T)
+csBoxplot(genes(cuff))
 
 csScatterMatrix(genes(cuff))
 
@@ -332,8 +333,8 @@ degs %>% count( sample_1, sample_2, sample_1_overex) %>% kable()
 
 
 #+ fig.height=nrow(contrasts)+2
-ggplot(degs, aes(paste(sample_1, "vs",  sample_2), fill=status)) + geom_bar() +xlab(NULL) + ylab("# DGEs") +ggtitle("DEGs by contrast") + coord_flip()
-ggplot(degs, aes(paste(sample_1, "vs",  sample_2), fill=sample_1_overex)) + geom_bar(position="dodge") + xlab(NULL) + ylab("# DGEs") + ggtitle("DEGs by direction") + coord_flip()
+#ggplot(degs, aes(paste(sample_1, "vs",  sample_2), fill=status)) + geom_bar() +xlab(NULL) + ylab("# DGEs") +ggtitle("DEGs by contrast") + coord_flip()
+ggplot(degs, aes(paste(sample_1, "vs",  sample_2), fill=sample_1_overex)) + geom_bar() + xlab(NULL) + ylab("# DGEs") + ggtitle("DEGs by contrast") + coord_flip()
 
 
 #' DEGs can be browsed in Excel using the exported table or via the embedded table browser. To enable the IGV links, you need to set the port in the IGV preferences to 3334.