fixed scale in b2 qc plot

chipseq_workflow/chipseq_utils.sh

@@ -45,15 +45,17 @@ write.delim(algnSummary, file="bowtie2_qc.txt")
 
 scale_fill_discrete <- function (...){ scale_color_brewer(..., type = "seq", palette="Set1", "fill", na.value = "grey50") }
 
+## make sure that mapping efficency is a ratio between 0 and 1
+algnSummary %<>% mutate(mapping_efficiency=mapping_efficiency/100.)
 
 #+ fig.height=nrow(algnSummary)
 ggplot(algnSummary, aes(condition, mapping_efficiency)) +
     geom_bar(stat="identity") +
-    ylim(0,100) +
     coord_flip() +
+    scale_y_continuous(labels=percent, limits=c(0,1))
     ggtitle("mapping efficiency")
 
-    ggplot(algnSummary, aes(condition, num_reads*mapping_efficiency)) +
+ggplot(algnSummary, aes(condition, num_reads*mapping_efficiency)) +
     geom_bar(stat="identity") +
     xlab("# alignments") +
     coord_flip() +