cosmetics

dge_workflow/cuffdiff_report.R

@@ -23,6 +23,7 @@ opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
 ## florio_11b: setwd("/lustre/projects/bioinfo/holger/projects/florio_11b/cuffdiff/dge_report"); opts <- docopt(doc, "--constrasts contrasts.txt --pcutoff 0.01 /projects/bioinfo/holger/projects/florio_11b/cuffdiff")
 # opts <- docopt(doc, "--undirected  ..")
 # opts <- docopt(doc, "..")
+# opts <- docopt(doc, "--pcutoff 0.05 ..")
 # opts <- docopt(doc, paste(Sys.getenv("DGE_PARAMS"), ".."))
 ## todo use commandArgs here!!
 #opts <- docopt(doc, paste(Sys.getenv("DGE_PARAMS"), paste(commandArgs(TRUE), collapse=" ")))
@@ -48,9 +49,9 @@ if(is.na(file.info(cuffdb_directory)$isdir)){
 }
 
 
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/bio/diffex_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
 
 #+ results='asis', echo=FALSE
 cat('
@@ -504,7 +505,7 @@ sigEnrResults %>% select(-Genes) %>% kable("html", table.attr = "class='dtable'"
 #	    print(logPlot)
 #})
 
-#+ include=FALSE
+#+ include=FALSE, error=TRUE
 warning("dropping levels")
 sigEnrResults %<>% mutate(Category=ac(Category)) ## drop unsused level to get consistent color palette