Add Functional Enrichment TSV Links to functional-enrichment.Rmd

[menoldmt]

Problem:

It would be convenient to have links to TSV files directly below functional enrichment plots. These files include dimensions, like GeneRatio, not otherwise shown in the plots.
 
Proposed Solution:

To ease data access, write enrichResults data to a file and add markdown links to the enrichResults TSV files below respective dotplot, emapplot, and cnetplots.
For this, introduce a function, print_table_link() here. This function will take the contrast 'name', the log fold change 'direction' and the 'ontology' from "enrich_list", save the file in the 'enrichResults/tables/' directory and generate relevant links as such:

   print_table_link <- function(name, direction, ont){
   # Make links to enrichResults table .tsv and all plots .pdf, and .png
   file_name_tsv <- paste0(name, '-', direction, '-', ont, '.tsv')
   dir.create('enrichResults/tables', recursive = TRUE)
   file_path_tsv <- file.path('enrichResults', 'tables', file_name_tsv)
   write.table(data.frame(enrich_list[[name]][[direction]][[ont]]),
     file = file_path_tsv,
     sep = "\t",
     quote = FALSE,
     row.names = FALSE,
     col.names = TRUE)

   mdcat('enrichResults data table:')
   mdcat('- [', file_name_tsv, ']', '(', file_path_tsv, ')')
 }

Add the following lines after here for dotplot for example:

       plot_type <- "dotplot"
       dotplot <- dotplot_list[[name]][[direction]][[ont]]
       print(dotplot)
       print_table_link(name, direction, ont)

File names should comprise of the contrast's 'name', 'direction' and 'ontology' used.
Call print_table_link() under each plot print statement to maintain appropriate links for each plot being printed here for dotplot, here for emapplot, and here for cnetplot

[esnaultc]

Noticed this issue while browsing, I have used an alternative solution that concatenates all contrasts into one table. Could use a combination of both solutions.

# get all combinations of up/down/changed and ontologies.
# All contrasts have the same GO results structure, so can use [[1]] to get the names
smry <- list()
for (direction in names(enrich_list[[1]])) {
  smry[[direction]] <- list()
  for (ont in names(enrich_list[[1]][[direction]])) {
    tmp <- lapply(names(enrich_list), function(x) {
      enrich_list[[x]][[direction]][[ont]] %>%
        as.data.frame() %>%
        mutate(contrast = x)
    })
  smry[[direction]][[ont]] <- do.call(rbind, tmp)
  }
}

# save and print links
dir.create('functional_enrichment_output', showWarnings = FALSE)

for (direction in names(smry)) {
  for (ont in names(smry[[direction]])) {
    fn <- paste0('functional_enrichment_output/', direction, '_', ont, '.tsv')
    write.table(smry[[direction]][[ont]],
      file=fn, row.names=FALSE, sep='\t', quote=FALSE)
    mdcat('- [', fn, '](', fn, ')')
  }
}