Commit c2046343 authored by Holger Brandl's avatar Holger Brandl

create session file after pathway vis

parent 7a440b21
......@@ -23,7 +23,7 @@ load_pack(knitr)
load_pack(DT)
results_prefix = if_else(exists("reportName"), reportName, "")
results_prefix = if(exists("reportName")) reportName else ""
## todo why is tidyr not processing an empty dataframe
keggPathways <- opts$pathways %>% str_split(",") %>% unlist()
......@@ -65,6 +65,7 @@ pwPlotDir = add_prefix("pathways_pngs")
dir.create(pwPlotDir)
plot_pathway <- function(pathwayID, sliceData){
# pathwayID="hsa04080"; sliceData <- sliceData
# pathwayID="mmu04015"; sliceData <- sliceData
# pathwayID="hsa04145"; sliceData <- sliceData
# browser()
......@@ -109,7 +110,9 @@ plot_pathway <- function(pathwayID, sliceData){
#keggPathways <- c("mmu00830")
pathwayPlots <- keggPathways %>% map(function(pathwayID){
pathwayPlots <- keggPathways %>%
# head(1) %>%
map(function(pathwayID){
# echo("processing pathway", pathwayID)
plot_pathway(pathwayID, sliceData)
})
......@@ -224,3 +227,6 @@ createImgMap <- function(plotData){
}
pathwayPlots %>% walk(createImgMap)
session::save.session(".plot_kegg_pathways.dat");
# session::restore.session(".plot_kegg_pathways.dat");
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