Commit 49891eaf authored by Holger Brandl's avatar Holger Brandl

use abs.max for gene aggregation

parent b31b589b
......@@ -20,14 +20,14 @@ 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/v1.22/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/bio/diffex_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.25/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.25/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.25/R/bio/diffex_commons.R")
require_auto(knitr)
require_auto(DT)
loadpack(knitr)
loadpack(DT)
require_auto(clusterProfiler)
loadpack(clusterProfiler)
#devtools::session_info() # nice!
......@@ -370,14 +370,15 @@ l_ply(term_barplot_files$file, function(pngFile){ cat(paste0("<img src='", pngFi
## todo why is tidyr not processing an empty dataframe
keggPathways <- enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique() # %>% head(3) ## todo remove debug head
##+ results='asis'
#if(!exists("keggPathways") | nrow(keggPathways)==0){
# cat("No enriched pathways found")
#}
require_auto(pathview)
require_auto(png)
require_auto(naturalsort)
loadpack(pathview)
loadpack(png)
loadpack(naturalsort)
# keggPathways <- keggPathways[1]
......@@ -406,11 +407,22 @@ pwPlotDir <-".pathways"
dir.create(pwPlotDir)
#Toxoplasmose debugging of 11796
#c(11796,11797,11798) %>%
# clusterProfiler::bitr(fromType="ENTREZID", toType="ENSEMBL", annoDb="org.Mm.eg.db") %>%
# set_names("entrez_gene_id", "ensembl_gene_id" ) %>%
# inner_join( sliceData %>% add_rownames("ensembl_gene_id") )
# session::save.session(".pview_debug.dat");
# session::restore.session(".pview_debug.dat");
plot_pathway <- function(pathwayID, sliceData){
# pathwayID="mmu04015"; sliceData <- sliceData
# pathwayID="mmu05145"; sliceData <- sliceData
# browser()
# echo("processing pathway", pathwayID)
pv.out <- pathview(
pv.out <- pathview(
# gene.data = sliceData %>% add_rownames("ensembl_gene_id") %>% tbl_df %>% filter(ensembl_gene_id %in% c("ENSMUSG00000073901", "ENSMUSG00000032000", "ENSMUSG00000021025")) %>% column2rownames("ensembl_gene_id"),
gene.data = sliceData,
pathway.id = pathwayID,
species = keggOrCode,
......@@ -418,7 +430,7 @@ plot_pathway <- function(pathwayID, sliceData){
# out.suffix = pathwayID,
multi.state = ncol(sliceData)>1,
# kegg.native=F,
# node.sum = "mean", # the method name to calculate node summary given that multiple genes or compounds are mapped to it
node.sum = "max.abs", # the method name to calculate node summary given that multiple genes or compounds are mapped to it
limit = list(gene = c(-4,4)),
gene.idtype="ensembl"
)
......@@ -434,10 +446,7 @@ plot_pathway <- function(pathwayID, sliceData){
system(paste("rm", paste0(pathwayID, ".xml"), paste0(pathwayID, ".png")))
## interactive plotting
# ima <- readPNG(outfile)
# plot.new()
# lim <- par()
# rasterImage(ima, lim$usr[1], lim$usr[3], lim$usr[2], lim$usr[4])
# ima <- readPNG(figuresPlotFile); plot.new(); lim <- par(); rasterImage(ima, lim$usr[1], lim$usr[3], lim$usr[2], lim$usr[4]);
pv.out$plotfile=figuresPlotFile
pv.out$pathway_id=pathwayID
......@@ -507,13 +516,19 @@ makeTooltip <- function(entrez_id){
#</style>
#")
pathwayName <- function(pathwayID, enrResults) enrResults %>% filter(ontology=="kegg") %>% filter(ID==pathwayID) %$% Description
#
## todo add tooltips with additinal info
## http://stackoverflow.com/questions/5478940/how-to-create-a-html-tooltip-on-top-of-image-map
## extended version with clickable links
createImgMap <- function(plotData){
#browser()
warning("compiling overlay toolips...")
# cat(paste0("pathway:", plotData$pathway_id) # todo rather show the pathway name here and create anhor list on top of section
# pathwayName("mmu05145", enrResults)
cat(paste0("<h3>",pathwayName(plotData$pathway_id, enrResults), "</h3>"))
#pngFile="mmu04015.pathview.png"
#plotData <- pathwayPlots[[1]]
#plotData <- unlist(pathwayPlots)
......
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