diff --git a/common/plot_kegg_pathways.R b/common/plot_kegg_pathways.R index 5a14366be9a540e4027c3276c09f5aec35c6aca8..cb28b232d90c02895987452eac560a4e9980bfed 100755 --- a/common/plot_kegg_pathways.R +++ b/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){