plot mroe terms

common/plot_kegg_pathways.R

@@ -13,18 +13,18 @@ Usage: plot_kegg_pathways.R <overlay_data_tsv> <pathways>...
 opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
 # opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
 
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/bio/diffex_commons.R")
+if(!require(devtools)) install.packages("devtools")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.21/R/bio/diffex_commons.R")
 
 require_auto(knitr)
 require_auto(DT)
-require_auto(readr)
 
 
 
 ## todo why is tidyr not processing an empty dataframe
-keggPathways <- opts$pathways
+keggPathways <- opts$pathways %>% str_split(",") %>% unlist()
 
 ##+ results='asis'
 #if(!exists("keggPathways") | nrow(keggPathways)==0){