Commit f77c2280 authored by Holger Brandl's avatar Holger Brandl
Browse files

removed plyr dependency

parent e759b13d
......@@ -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
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment