impl replicate merging

dge_workflow/fastqc_summary.R

@@ -67,7 +67,7 @@ readSummary <- function(statsFile){
 
 qcSummary <- list.files(path=baseDir, pattern="^summary.txt", full.names=TRUE, recursive=T) %>%  ldply(readSummary)
 
-
+#+ fig.height=20
 qcSummary %>% ggplot(aes(score, run, fill=tolower(flag))) +
     geom_tile() +
     rotXlab() +
@@ -98,6 +98,7 @@ baseQualities <- fastqDataFiles %>%  ldply(readBaseQualDist)
 #with(baseQualities, as.data.frame(table(run)))
 
 
+#+ fig.height=20
 baseQualities %>% ggplot(aes(reorder(Base, base_order), Mean, group=run, color=run)) + geom_line() + scale_y_continuous(limits=c(2, 40))