finished new tophat mapping report

bash/bioinfo_utils.sh

 
-#### Tophat Mapping Report from the logs
+## Tophat Mapping Report from the logs
 TophatMappingReport(){
-## todo replace source with simple R script as for bowtie-report
 echo '
-devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/deepseq/ngs_tools.R")
-createMappingReport()
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
+
+
+parseAlgnSummary_T2_0_11 <- function(alignSummary){
+    #alignSummary="/projects/bioinfo/holger/projects/marta_rnaseq/human_leipzig/mapping/S5382_aRG_1b_rep1/align_summary.txt"
+    algnData <- readLines(alignSummary)
+
+    data.frame(
+        condition=basename(dirname(alignSummary)),
+        num_reads=as.numeric(str_match(algnData[2], " ([0-9]*$)")[,2]),
+        mapped_reads=100*as.numeric(str_match(algnData[3], ":[ ]*([0-9]*) ")[,2][1])
+    ) %>% transform(mapping_efficiency=mapped_reads/num_reads)
+}
+
+
+algnSummary <- ldply(list.files(".", "align_summary.txt", full.names=TRUE, recursive=T), parseAlgnSummary_T2_0_11, .progress="text")
+write.delim(algnSummary, file="tophat_mapping_stats.txt")
+
+scale_fill_discrete <- function (...){ scale_color_brewer(..., type = "seq", palette="Set1", "fill", na.value = "grey50") }
+
+
+projectName=basename(dirname(getwd()))
+
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/mdreport/master/R/mdreport-package.r")
+
+md_new(paste("Mapping Summary for ", projectName))
+
+
+md_plot(ggplot(algnSummary, aes(condition, mapping_efficiency)) + geom_bar(stat="identity") +coord_flip() + ylim(0,100) + ggtitle("mapping efficiency"))
+
+md_plot(ggplot(algnSummary, aes(condition, num_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle("read counts") +scale_y_continuous(labels=comma))
+
+md_plot(ggplot(algnSummary, aes(condition, mapped_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle("alignments counts") +scale_y_continuous(labels=comma))
+
+
+#ggplot(melt(algnSummary), aes(condition, value)) + geom_bar(stat="identity") +facet_wrap(~variable, scales="free") + ggtitle("mapping summary") + scale_y_continuous(labels=comma)  + theme(axis.text.x=element_text(angle=90, hjust=0))
+#ggsave2(w=10, h=10, p="mapstats")
+
+
+md_report("tophat_mapping_report", open=F)
 ' | R -q --vanilla
 }
 export -f TophatMappingReport

bash/test.R

-devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
-devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
-
-
-
-
-parseAlgnSummary_T2_0_11 <- function(alignSummary){
-    #alignSummary="/projects/bioinfo/holger/projects/marta_rnaseq/human_leipzig/mapping/S5382_aRG_1b_rep1/align_summary.txt"
-    algnData <- readLines(alignSummary)
-
-    data.frame(
-        condition=basename(dirname(alignSummary)),
-        num_reads=as.numeric(str_match(algnData[2], " ([0-9]*$)")[,2]),
-        mapped_reads=100*as.numeric(str_match(algnData[3], ":[ ]*([0-9]*) ")[,2][1])
-    ) %>% transform(mapping_efficiency=mapped_reads/num_reads)
-}
-
-
-algnSummary <- ldply(list.files(".", "align_summary.txt", full.names=TRUE, recursive=T), parseAlgnSummary_T2_0_11, .progress="text")
-write.delim(algnSummary, file="tophat_mapping_stats.txt")
-
-scale_fill_discrete <- function (...){ scale_color_brewer(..., type = "seq", palette="Set1", "fill", na.value = "grey50") }
-
-
-projectName=basename(dirname(getwd()))
-
-ggplot(algnSummary, aes(condition, mapping_efficiency)) + geom_bar(stat="identity") +coord_flip() + ylim(0,100) + ggtitle(concat("mapping efficiency in ", projectName))
-ggsave2(width=12)
-
-ggplot(algnSummary, aes(condition, num_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle(concat("read counts in", projectName)) +scale_y_continuous(labels=comma)
-ggsave2(width=12)
-
-ggplot(algnSummary, aes(condition, mapped_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle(concat("alignments in", projectName)) +scale_y_continuous(labels=comma)
-ggsave2(width=12)
-
-
-ggplot(melt(algnSummary), aes(condition, value)) + geom_bar(stat="identity") +facet_wrap(~variable, scales="free") + ggtitle("mapping summary") + scale_y_continuous(labels=comma)  + theme(axis.text.x=element_text(angle=90, hjust=0))
-ggsave2(w=10, h=10, p="mapstats")
-
-