fixed missing slice model table

common/cp_enrichment.R

@@ -20,10 +20,10 @@ 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/v1.36/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.36/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.36/R/bio/cp_utils.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.36/R/bio/diffex_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/bio/cp_utils.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/bio/diffex_commons.R")
 
 load_pack(knitr)
 load_pack(DT)
@@ -317,10 +317,14 @@ walk(term_barplot_files$file, function(pngFile){ cat(paste0("<img src='", pngFil
 keggPathways <- enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique() # %>% head(3) ## todo remove debug head
 
 
-# results='asis'
+## #+ results='asis', echo=FALSE
 if(!exists("keggPathways") || length(keggPathways)==0){
    cat("No enriched pathways found")
-}else{
+    return()
+    quit()
+}
+
+
 
 load_pack(naturalsort)
 
@@ -351,7 +355,8 @@ sliceData <- overlayData %>% rify_names() %>% select_(., .dots=naturalsort(ac(na
 
 #sliceData %>% head %>% kable()
 
-data.frame(set=names(sliceData)) %>% mutate(slice_index=row_number()) %>% kable()
+data.frame(set=names(sliceData)) %>% mutate(slice_index=row_number()) %>% knitr::kable()
+
 
 pwPlotDir <-".pathways"
 
@@ -469,7 +474,7 @@ makeTooltip <- function(entrez_id){
 
 
 
-## #+ results="asis", echo=FALSE
+#+ results="asis", echo=FALSE
 
 ## simple non-clickable plots
 ## http://stackoverflow.com/questions/12588323/r-how-to-extract-values-for-the-same-named-elements-across-multiple-objects-of
@@ -540,7 +545,7 @@ pathwayPlots %>% plyr::l_ply(createImgMap)
 ## respin it for cild inclusion
 # require(knitr); setwd("/Volumes/projects/bioinfo/scripts/ngs_tools/dev/common"); spin("cp_enrichment.R", knit=F)
 
-}
+# }
 
 #' ## Notes
 #' Other interesting tools to perform enrichment testing