Merge branch 'master' of ssh://git-srv1/local/git/bioinformatics

dge_workflow/dge_analysis.R

@@ -42,7 +42,7 @@ devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/
 devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
 
 require(cummeRbund)
-devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/bio/cummerutils.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/bio/diffex_commons.R")
 
 #knitr::opts_knit$set(root.dir = getwd())
 
@@ -286,62 +286,12 @@ save(degs, file=".degs.RData")
 #' ## Term enrichment
 #+ echo=FALSE
 
-#fpkmMatrix(genes(cuff)) %>% head()
-
-ontologies <- c(
-    "GOTERM_CC_FAT",
-    "GOTERM_MF_FAT",
-    "GOTERM_BP_FAT",
-
-    "PANTHER_PATHWAY",
-    "REACTOME_PATHWAY",
-    "KEGG_PATHWAY",
-
-    "GOTERM_CC_FAT",
-    "GOTERM_MF_FAT",
-    "GOTERM_BP_FAT"
-)
-
 #' This analysis was performed using [David](http://david.abcc.ncifcrf.gov/). The following ontologies were tested: `r paste(ontologies, collapse=', ')`
 
-require(RDAVIDWebService) ## just works if installed on non-network-drive (e.g. /tmp/)
-
 geneLists <- degs %>%
 #    transmute(ensembl_gene_id, list_id=paste(sample_1, "vs", sample_2, "ovex", sample_1_overex, sep="_"))
     transmute(ensembl_gene_id, list_id=paste(sample_1, "vs", sample_2))
 
-
-## http://www.bioconductor.org/packages/release/bioc/vignettes/RDAVIDWebService/inst/doc/RDavidWS-vignette.pdf
-## e.g. getClusterReport --> plot2D
-
-
-davidAnnotationChart <- function(someGenes){ ## expexted to have a column with gene_id
-#    echo("processing list with", length(someGenes), "genes")
-#    someGenes <- degs$ensembl_gene_id
-
-
-    if(length(someGenes)>1500){
-        someGenes <- sample(someGenes) %>% head(1500)
-    }
-
-    david<-DAVIDWebService$new(email="brandl@mpi-cbg.de")
-
-#    getTimeOut(david)
-    setTimeOut(david, 80000) ## http://www.bioconductor.org/packages/release/bioc/vignettes/RDAVIDWebService/inst/doc/RDavidWS-vignette.pdf
-
-    result<-addList(david, someGenes, idType="ENSEMBL_GENE_ID", listName=paste0("list_", sample(10000)[1]), listType="Gene")
-
-    david %>% setAnnotationCategories(ontologies)
-
-    annoChart <-getFunctionalAnnotationChart(david)
-
-#    clusterReport <-getClusterReport(david)
-
-    return(annoChart %>% subset(select=-Genes))
-}
-
-
-
 grpdDegs <- if(split_hit_list){
     degs %>% group_by(sample_1, sample_2, sample_1_overex)
 }else{
@@ -350,6 +300,7 @@ grpdDegs <- if(split_hit_list){
 
 enrResults <- grpdDegs %>% do(davidAnnotationChart(.$ensembl_gene_id))
 
+
 write.delim(enrResults, file="enrResults.txt")
 # enrResults <- read.delim("enrResults.txt")
 #'  [Enrichment Results](enrResults.txt)

dge_workflow/dge_utils.sh

@@ -287,7 +287,7 @@ cp -r . $tmpDbDir
 genome=$(echo $gtfFile | cut -f7 -d'/'); echo "genome is $genome"
 
 ## make sure to use temp-r to avoid file locking problems
-R_LIBS=/tmp/r_index
+export R_LIBS=/tmp/r_index
 
 echo '
 require(cummeRbund)

misc/spin.R

@@ -70,8 +70,19 @@ cssHeader='
       max-width: 90%;
   }
 </style>
+
+
+<!-- add jquery datatable support -->
+<link rel="stylesheet" type="text/css" href="http://cdn.datatables.net/1.10.4/css/jquery.dataTables.css">
+<script type="text/javascript" charset="utf8" src="http://code.jquery.com/jquery-2.1.2.min.js"></script>
+<script type="text/javascript" charset="utf8" src="http://cdn.datatables.net/1.10.4/js/jquery.dataTables.js"></script>
 '
 
+#<!-- add bootstrap support -->
+#<link href="http://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/css/bootstrap.min.css" rel="stylesheet">
+#<script src="http://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/js/bootstrap.min.js"></script>
+
+
 ## custom title http://stackoverflow.com/questions/14124022/setting-html-meta-elements-with-knitr
 opts_chunk$set(
     cache = spin_opts$c,

misc/spin_utils.sh

+
+spinsnip(){
+    if [ $# -ne 1 ]; then
+         >&2 echo "Usage: spinsnip <report name> [other args]*"
+        return
+    fi
+
+    reportName=$1
+    tmpR=$(echo $reportName | tr " " "_").R
+
+    ## http://stackoverflow.com/questions/11454343/pipe-output-to-bash-function
+    cat | sed 's/#>/#'"'"'/g'  > $tmpR
+
+    echo "spining $tmpR..."
+
+    shift
+    spin.R $tmpR $*
+
+    rm $tmpR
+}