TGx-HDACi reporting module (#252)

* add tgx-hdaci report module

* make tgx-hdaci report work in pipeline

* fix gene names for hwt2.0

* fix typo

* use ensembl IDs not gene symbols

* uncomment summarize_across_facet lines

* improve gene mismatch messages

* tgx-hdaci for human datasets only

* move bibtex files to their own folder

R.ODAF.utils/R/write_reports.R

@@ -127,3 +127,28 @@ make_tgxddi_reports <- function(pars, paths, facet) {
     render_report(tgxddi_report, tgxddi_file, pars)
   }
 }
+
+#' Generate TGx-HDACi Report
+#'
+#' Renders the TGx-HDACi report HTML file for a given facet using the specified parameters.
+#' The function updates the `reports_filter` in `pars` based on the facet provided.
+#'
+#' @param pars A list of parameters used for report generation.
+#' @param facet A character string specifying the facet for which to generate the report.
+#' @param paths A list of paths used throughout the analysis.
+#' @return Invisible NULL. The function is called for its side effect of rendering an HTML report.
+#' @export
+make_hdaci_reports <- function(pars, paths, facet) {
+  if (is.na(pars$deseq_facet) && is.na(pars$reports_facet)) {
+    pars$reports_filter <- NULL
+  } else {
+    pars$reports_filter <- facet
+  }
+  prefix <-get_prefix(prefix_pars = pars, prefix_facet = facet)
+  if (pars$generate_tgxhdaci_report) {
+    message("Generating TGX-HDACi report")
+    tgxhdaci_report <- file.path(paths$projectdir, "Rmd", "tgx-hdaci.Rmd")
+    tgxhdaci_file <- file.path(paths$reports_dir, paste0("tgxhdaci_", prefix, ".html"))  
+    render_report(tgxhdaci_report, tgxhdaci_file, pars)
+  }
+}

Rmd/DESeq2_report_new.Rmd

@@ -57,6 +57,7 @@ params:
   generate_data_explorer_report: TRUE
   generate_go_pathway_report: TRUE
   generate_tgxddi_report: TRUE
+  generate_tgxhdaci_report: TRUE
   output_digits: 5
   parallel: FALSE
   species_data: null
@@ -74,7 +75,7 @@ output:
     code_folding: hide
     theme: spacelab           # flatly spacelab sandstone cerulean
     code_download: true
-bibliography: "`r file.path(params$projectdir, 'Rmd/references.bib')`"
+bibliography: "`r file.path(params$projectdir, 'references/references.bib')`"
 
 ---
 

Rmd/Sample_QC.Rmd

@@ -43,7 +43,7 @@ output:
     code_folding: hide
     theme: spacelab           # flatly spacelab sandstone cerulean
     code_download: true
-bibliography: "`r file.path(params$projectdir, 'Rmd/references.bib')`"
+bibliography: "`r file.path(params$projectdir, 'references/references.bib')`"
 ---
 
 ```{r setup, include=FALSE}

Rmd/data_explorer_report.Rmd

@@ -57,6 +57,7 @@ params:
   generate_data_explorer_report: TRUE
   generate_go_pathway_report: TRUE
   generate_tgxddi_report: TRUE
+  generate_tgxhdaci_report: TRUE
   output_digits: 5
   parallel: FALSE
   species_data: null

Rmd/go_pathway_report.Rmd

@@ -57,6 +57,7 @@ params:
   generate_data_explorer_report: TRUE
   generate_go_pathway_report: TRUE
   generate_tgxddi_report: TRUE
+  generate_tgxhdaci_report: TRUE
   output_digits: 5
   parallel: FALSE
   species_data: null

Rmd/stats_report.Rmd

@@ -57,6 +57,7 @@ params:
   generate_data_explorer_report: TRUE
   generate_go_pathway_report: TRUE
   generate_tgxddi_report: TRUE
+  generate_tgxhdaci_report: TRUE
   output_digits: 5
   parallel: FALSE
   species_data: null