fixed package loading for R3.3

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/v1.25/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")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/bio/diffex_commons.R")
 
 loadpack(knitr)
 loadpack(DT)
 
-loadpack(clusterProfiler)
+#loadpack(clusterProfiler)
 
 #devtools::session_info() # nice!
 
@@ -63,7 +63,7 @@ resultsBaseName <- if(str_length(opts$project)>0) paste0(opts$project, ".") else
 qCutoff <- as.numeric(opts$qcutoff)
 
 
-reload_dplyr()
+#reload_dplyr()
 
 ########################################################################################################################
 #' ## Enrichment Analysis
@@ -139,7 +139,7 @@ annoDb <- guess_anno_db(geneLists$ensembl_gene_id) # e.g. "org.Hs.eg.db"
 
 ## convert to entrez gene ids
 
-glMappedRaw <-  clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", annoDb=annoDb) %>%
+glMappedRaw <-  clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEMBL", toType="ENTREZID", OrgDb=annoDb) %>%
     set_names("ensembl_gene_id", "entrez_gene_id") %>% right_join(geneLists)
 
 
@@ -147,6 +147,11 @@ glMappedRaw <-  clusterProfiler::bitr(geneLists$ensembl_gene_id, fromType="ENSEM
 #' Check how many failed to map
 count(glMappedRaw, is.na(entrez_gene_id))
 
+unloadNamespace('clusterProfiler')
+#loadpack(clusterProfiler)
+
+reload_dplyr()
+
 glMapped <- glMappedRaw %>% filter(!is.na(entrez_gene_id)) %>% select(-ensembl_gene_id)  %>%
     ## regroup the data
     #    group_by_(cluster)
@@ -158,11 +163,11 @@ glMapped <- glMappedRaw %>% filter(!is.na(entrez_gene_id)) %>% select(-ensembl_g
 #count(glMappedSub, cluster)
 
 ## sync reactome pacakge to node
-if(Sys.getenv("LSF_SERVERDIR")!="" && dir.exists("/tmp/local_r_packages")){
-    system("if [ ! -d '/tmp/local_r_packages/reactome.db/' ]; then scp -r falcon:/tmp/local_r_packages /tmp ; fi")
-}
+#if(Sys.getenv("LSF_SERVERDIR")!="" && dir.exists("/tmp/local_r_packages")){
+#    system("if [ ! -d '/tmp/local_r_packages/reactome.db/' ]; then scp -r falcon:/tmp/local_r_packages /tmp ; fi")
+#}
 
-require_auto(ReactomePA)
+loadpack(ReactomePA)
 
 cp_test <- function(geneIds){
     # DEBUG geneIds <- glMapped %>% filter(cluster %in% c("cluster_9")) %$% entrez_gene_id %>% as.integer
@@ -179,11 +184,11 @@ cp_test <- function(geneIds){
 
 #    browser()
 #    pantherResults <-     enricher(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, TERM2GENE = PANTHER10_ontology) %>% summary()
-    keggResults <-        enrichKEGG(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, use_internal_data=T) %>% summary()
-    reactomeResults <- enrichPathway(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE) %>% summary()
-    goResultsCC <-          enrichGO(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, ont = "CC") %>% summary()
-    goResultsMF <-          enrichGO(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, ont = "MF") %>% summary()
-    goResultsBP <-          enrichGO(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, readable = TRUE, ont = "BP") %>% summary()
+    keggResults <-        clusterProfiler::enrichKEGG(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff, use_internal_data=T) %>% summary()
+    reactomeResults <-      enrichPathway(gene = geneIds, organism = cpSpecies, qvalueCutoff = qCutoff) %>% summary()
+    goResultsCC <-          clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = qCutoff, ont = "CC") %>% summary()
+    goResultsMF <-          clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = qCutoff, ont = "MF") %>% summary()
+    goResultsBP <-          clusterProfiler::enrichGO(gene = geneIds, OrgDb = annoDb, qvalueCutoff = qCutoff, ont = "BP") %>% summary()
 
     #cp-bug: if no pathways are enriched odd strucuture is retured ##todo file issue
     if(!("data.frame" %in% class(keggResults))) keggResults <- filter(goResultsBP, Description="foobar")
@@ -211,7 +216,7 @@ enrResults <-  quote(glMapped %>% do(cp_test(.$entrez_gene_id))) %>% cache_it(pa
 #}, .progress="text", .parallel=F) ##%>% cache_it(paste0("enrdata_", digest(glMapped)))
 #rbind_all(enrResults)
 
-reload_dplyr()
+#reload_dplyr()
 
 #enrResults %<>% rename(Category=Description)
 #enrResults %<>% rename(ontology=Category)
@@ -223,7 +228,7 @@ write_tsv(enrResults, path=paste0(resultsBaseName, "enrResults.txt"))
 # enrResults <- read.delim(paste0(resultsBaseName, "enrResults.txt"))
 #'  [Enrichment Results](`r paste0(resultsBaseName, "enrResults.txt")`)
 
-require_auto(DT)
+loadpack(DT)
 datatable(enrResults)
 
 #enrResults %>% ggplot(aes(pvalue)) + geom_histogram() + scale_x_log10()
@@ -376,10 +381,14 @@ keggPathways <- enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique()
 #    cat("No enriched pathways found")
 #}
 
-loadpack(pathview)
-loadpack(png)
 loadpack(naturalsort)
 
+
+#reload_dplyr()
+
+#unloadNamespace('pathview')
+
+
 # keggPathways <- keggPathways[1]
 
 #if(nrow(keggPathways)==0){
@@ -413,12 +422,34 @@ dir.create(pwPlotDir)
 #    set_names("entrez_gene_id", "ensembl_gene_id" ) %>%
 #    inner_join( sliceData %>% add_rownames("ensembl_gene_id") )
 
+# install.packages("session")
 # session::save.session(".pview_debug.dat");
 # session::restore.session(".pview_debug.dat");
 
+## from http://stackoverflow.com/questions/7505547/detach-all-packages-while-working-in-r
+## todo remove this once we use v1.27 of core_commons
+detachAllPackages <- function() {
+    basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")
+    package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]
+    package.list <- setdiff(package.list,basic.packages)
+    if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE)
+}
+detachAllPackages()
+
+
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
+#loadpack(plyr)
+#loadpack(dplyr)
+#loadpack(dplyr)
+#loadpack(stringr)
+loadpack(pathview)
+loadpack(png)
+
+
+
 plot_pathway <- function(pathwayID, sliceData){
 #    pathwayID="mmu04015"; sliceData <- sliceData
-#    pathwayID="mmu05145"; sliceData <- sliceData
+#    pathwayID="mmu05216"; sliceData <- sliceData
 #    browser()
 #    echo("processing pathway", pathwayID)
      pv.out <- pathview(
@@ -480,6 +511,8 @@ pathwayPlots <- pathwayPlots[lapply(pathwayPlots, is.character) == 0]
 stopifnot(llply(pathwayPlots, function(x) file.exists(x$plotfile)) %>% unlist %>% all)
 
 
+.instpack("biomaRt")
+
 ## prepare tooltips with expression scores
 ens2entrez <- quote({
 #    mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))