removed plyr dependency

common/cp_enrichment.R

@@ -20,7 +20,8 @@ Options:
 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/v1.39/R/core_commons.R")
+coreCommons="https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/core_commons.R"
+devtools::source_url(coreCommons)
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/ggplot_commons.R")
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/bio/cp_utils.R")
 devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/bio/diffex_commons.R")
@@ -28,8 +29,6 @@ devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v
 load_pack(knitr)
 load_pack(DT)
 
-#load_pack(clusterProfiler)
-
 #devtools::session_info() # nice!
 
 ## to fix child support issue with knitr, see also
@@ -307,8 +306,12 @@ walk(term_barplot_files$file, function(pngFile){ cat(paste0("<img src='", pngFil
 #+ eval=(!is.null(opts$overlay_expr_data) & (nrow(enrResults %>% filter(ontology=="kegg")) >0))
 
 ## todo why is tidyr not processing an empty dataframe
-keggPathways <- enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique() # %>% head(3) ## todo remove debug head
+keggPathways = enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique() # %>% head(3) ## todo remove debug head
+
 
+## remove mmu04723 if present (see bug report https://support.bioconductor.org/p/95354/)
+# keggPathways = c("mmu04660", "mmu03060", "mmu04110", "mmu04260", "mmu04723", "mmu05322", "mmu04114")
+keggPathways %<>% purrr::discard(~ .=="mmu04723") ## overloaded by scales packages
 
 ## #+ results='asis', echo=FALSE
 if(!exists("keggPathways") || length(keggPathways)==0){
@@ -340,7 +343,6 @@ keggOrCode <- guess_pathview_species(geneLists$ensembl_gene_id)
 #sliceData <- overlayData %>% column2rownames("ensembl_gene_id")
 
 ## sort slices in natural order
-rify_names  <- function(df){ names(df) <- names(df) %>% str_replace_all(" ", "_"); df}
 overlayData %<>% select_(., .dots=naturalsort(ac(names(.))))
 sliceData <- overlayData %>% column2rownames("ensembl_gene_id")
 
@@ -363,26 +365,21 @@ dir.create(pwPlotDir)
 #    inner_join( sliceData %>% add_rownames("ensembl_gene_id") )
 
 # install.packages("session")
-# session::save.session(".pview_debug.dat");
-# session::restore.session(".pview_debug.dat");
+# session::save.session(".cp_enrichment.debug.dat");
+# session::restore.session(".cp_enrichment.debug.dat");
 
 ## from http://stackoverflow.com/questions/7505547/detach-all-packages-while-working-in-r
 unload_packages()
 
-
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
-#load_pack(plyr)
-#load_pack(dplyr)
-#load_pack(dplyr)
-#load_pack(stringr)
+devtools::source_url(coreCommons)
 load_pack(pathview)
 load_pack(png)
 
 
-
 plot_pathway <- function(pathwayID, sliceData){
 #    pathwayID="mmu04015"; sliceData <- sliceData
 #    pathwayID="mmu05216"; sliceData <- sliceData
+#    pathwayID="mmu04723"; sliceData <- sliceData
 #    browser()
 #    echo("processing pathway", pathwayID)
      pv.out <- pathview(
@@ -422,12 +419,15 @@ plot_pathway <- function(pathwayID, sliceData){
 #keggPathways <- c("mmu00830")
 
 
+capture.output
 
+#+ echo=FALSE, warning=FALSE
 pathwayPlots <- keggPathways %>%
-#    head(3) %>%
-    llply(function(pathwayID){
-    plot_pathway(pathwayID, sliceData)
-})
+    # head(3) %>%
+    map(function(pathwayID){
+        # echo("processing pathway", pathwayID)
+        plot_pathway(pathwayID, sliceData)
+    })
 
 
 #save(pathwayPlots, file=".pathwayPlots.RData")
@@ -441,10 +441,10 @@ pathwayPlots <- pathwayPlots[lapply(pathwayPlots, is.character) == 0]
 
 
 ## make sure that all files exist
-stopifnot(llply(pathwayPlots, function(x) file.exists(x$plotfile)) %>% unlist %>% all)
+stopifnot(map_lgl(pathwayPlots, ~ file.exists(.$plotfile))  %>% all)
 
 
-.instpack("biomaRt")
+install_package("biomaRt")
 
 ## prepare tooltips with expression scores
 ens2entrez <- quote({
@@ -543,4 +543,9 @@ pathwayPlots %>% plyr::l_ply(createImgMap)
 
 #' ## Notes
 #' Other interesting tools to perform enrichment testing
-#' * [piano](http://www.bioconductor.org/packages/release/bioc/html/piano.html)
\ No newline at end of file
+#' * [piano](http://www.bioconductor.org/packages/release/bioc/html/piano.html)
+
+#' System info:
+#+ results="asis"
+
+devtools::session_info()
\ No newline at end of file