cont. chipseq qc

chipseq_workflow/chipseq_utils.sh

@@ -49,24 +49,31 @@ scale_fill_discrete <- function (...){ scale_color_brewer(..., type = "seq", pal
 #+ fig.height=nrow(algnSummary)
 ggplot(algnSummary, aes(condition, mapping_efficiency)) +
     geom_bar(stat="identity") +
-    coord_flip() +
     ylim(0,100) +
+    coord_flip() +
     ggtitle("mapping efficiency")
 
 ggplot(algnSummary, aes(condition, num_reads)) +
     geom_bar(stat="identity") +
     coord_flip() +
-    ggtitle("read counts") +scale_y_continuous(labels=comma)
+    ggtitle("read counts") +
+    scale_y_continuous(labels=comma)
 
 ggplot(algnSummary, aes(condition, unique_mapper_prop)) +
-    geom_bar(stat="identity") + coord_flip() +
+    geom_bar(stat="identity") +
+    coord_flip() +
     ggtitle("unique-mapper proportions") +
-    scale_y_continuous(labels=comma)
+    scale_y_continuous(labels=percent) +
+    ylim(0,100)
+
 
 ggplot(algnSummary, aes(condition, multi_mappers_prop)) +
-    geom_bar(stat="identity") + coord_flip() +
+    geom_bar(stat="identity") +
+    coord_flip() +
     ggtitle("multi-mapper proportions") +
-    scale_y_continuous(labels=comma)
+    scale_y_continuous(labels=percent) +
+    ylim(0,100)
+
 
 #> ## Bam Correlation
 

dge_workflow/dge_utils.sh

@@ -5,8 +5,7 @@
 source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/lsf_utils.sh 2>&1 2>/dev/null)
 
 ## enable snippet spinning
-source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/R/utils/spinr.sh 2>&1 2>/dev/null)
-
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
 
 ## define common binaries
 export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.2:$PATH

dge_workflow/fastqc_summary.R

@@ -52,7 +52,7 @@ readCount <- function(statsFile){
 readCounts <- fastqDataFiles %>% ldply(readCount) # %>% print_head()
 
 require.auto(scales)
-#+ fig.width=12, fig.height=round(nrow(readCounts)/3)
+#+ fig.width=12, fig.height=round(nrow(readCounts)/2)
 ggplot(readCounts, aes(run, num_reads)) + geom_bar(stat="identity") + coord_flip() + scale_y_continuous(labels=comma) + ggtitle("read counts")
 
 # #+ results='asis'
@@ -75,7 +75,7 @@ readSummary <- function(statsFile){
 qcSummary <- fastqDataFiles %>%  ldply(readSummary)
 
 #' # Base Quality Distribution Summary
-#+ fig.height=2+round(nrow(readCounts)/3), fig.width=12
+#+ fig.height=2+round(nrow(readCounts)/2), fig.width=12
 qcSummary %>% ggplot(aes(score, run, fill=tolower(flag))) +
     geom_tile() +
     rotXlab() +
@@ -94,7 +94,7 @@ dupLevels <- fastqDataFiles %>% ldply(function(statsFile){
 })
 
 require.auto(scales)
-#+ fig.width=12, fig.height=round(nrow(dupLevels)/3)
+#+ fig.width=12, fig.height=round(nrow(dupLevels)/2)
 ggplot(dupLevels, aes(run, dedup_proportion)) + geom_bar(stat="identity") + coord_flip() + scale_y_continuous(labels=percent) + ggtitle("unique_reads/total_reads") + ylim(0,1)
 
 
@@ -133,7 +133,7 @@ baseQualities %>% ggplot(aes(reorder(Base, base_order), Mean, group=run, color=r
 
 runs <- with(baseQualities, as.data.frame(table(run)))
 
-#+ warning=FALSE, fig.width=15, fig.height=3*ceiling(nrow(runs)/3)
+#+ warning=FALSE, fig.width=15, fig.height=3*ceiling(nrow(runs)/2)
 
 ## http://stackoverflow.com/questions/12518387/can-i-create-an-empty-ggplot2-plot-in-r
 baseQualities %>%