use abs.max for gene aggregation

common/cp_enrichment.R

@@ -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)