Commit 43b8e6fb authored by Holger Brandl's avatar Holger Brandl

fixed missing slice model table

parent f864e445
......@@ -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
......
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