Cleanup, updated changelog, fixed output docs

CHANGELOG.md

@@ -31,7 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#159](https://github.com/nf-core/differentialabundance/issues/159)] - CUSTOM/MATRIXFILTER module update ([@WackerO](https://github.com/WackerO), review by [@suzannejin](https://github.com/suzannejin))
 - [[#154](https://github.com/nf-core/differentialabundance/issues/154)] - RMARKDOWNNOTEBOOK env update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#151](https://github.com/nf-core/differentialabundance/issues/151)] - Module update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - RMARKDOWNNOTEBOOK env update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - RMARKDOWNNOTEBOOK env update, SHINYNGS and CUSTOM update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ## v1.2.0 - 2023-04-19
 

assets/differentialabundance_report.Rmd

@@ -241,16 +241,16 @@ assay_names <- simpleSplit(params$exploratory_assay_names)
 names(assay_names) = assay_names
 assay_files <- lapply(assay_names, function(x) params[[paste0(x, '_matrix')]])
 
-assay_data <- lapply(c(1:length(assay_files)), function(x) {
+assay_data <- lapply(assay_files, function(x) {
   mat <- na.omit(
     read_matrix(
-      assay_files[[x]],
+      x,
       sample_metadata = observations,
       row.names = 1
     )
   )
   colnames(mat) <- observations[[params$observations_name_col]][match(colnames(mat), rownames(observations))]
-  mat
+  mat 
 })
 
 if (!is.null(params$features_log2_assays)) {
@@ -259,9 +259,6 @@ if (!is.null(params$features_log2_assays)) {
   assay_data <- cond_log2_transform_assays(assay_data, features_log2_assays)
 }
 
-# Lapply does not go over the assay_files themselves anymore, so we need to specifically assign their names to the data
-names(assay_data) <- names(assay_files)
-
 # Now we can rename the observations rows using the title field
 rownames(observations) <- observations[[params$observations_name_col]]
 
@@ -604,7 +601,6 @@ for (assay_type in rev(names(assay_data))){
     variable_genes <- selectVariableGenes(matrix = assay_data[[assay_type]], ntop = params$exploratory_n_features)
 
     dendroColorScale <- makeColorScale(length(unique(observations[[iv]])), palette = params$exploratory_palette_name)
-
     p <- clusteringDendrogram(
       2^assay_data[[assay_type]][variable_genes, ],
       observations[, iv, drop = FALSE],

docs/output.md

@@ -38,10 +38,10 @@ Stand-alone graphical outputs are placed in this directory. They may be useful i
   - `gsea/`: Directory containing graphical outputs from GSEA (where enabled). Plots are stored in directories named for the associated contrast.
     - `[contrast]/png/[gsea_plot_type].png`
   - `proteus/`: If `--study_type maxquant`: Directory containing plots produced by the proteus module which is used for processing MaxQuant input. Files are prefixed with the associated contrast and chosen normalization function (if any).
-    - `[contrast].proteus.[norm_function].normalized_dendrogram.png`: A sample clustering dendrogram after normalization, if chosen.
-    - `[contrast].proteus.[norm_function].normalized_mean_variance_relationship.png`: Plots of log intensity vs mean log intensity after normalization of each contrast level, if chosen.
-    - `[contrast].proteus.[norm_function].normalized_distributions.png`: A plot of sample distributions after normalization, if chosen.
-    - `[contrast].proteus.raw_distributions.png`: A plot of sample distributions without normalization.
+    - `[contrast]/[norm_function].normalized_dendrogram.png`: A sample clustering dendrogram after normalization.
+    - `[contrast]/[norm_function].normalized_mean_variance_relationship.png`: Plots of log intensity vs mean log intensity after normalization of each contrast level.
+    - `[contrast]/[norm_function].normalized_distributions.png`: A plot of sample distributions after normalization.
+    - `[contrast]/raw_distributions.png`: A plot of sample distributions without normalization.
 
 </details>
 
@@ -67,8 +67,8 @@ Most plots are included in the HTML report (see above), but are also included in
   - `gsea/`: Directory containing tables of differential gene set analyis from GSEA (where enabled)
     - `[contrast]/[contrast].gsea_report_for_[condition].tsv`: A GSEA report table for each side of each contrast
   - `proteus/`: If `--study_type maxquant`: Directory containing abundance values produced by the proteus module which is used for processing MaxQuant input. Files are prefixed with the associated contrast and chosen normalization function (if any).
-    - `[contrast].proteus.[norm_function].normalized_proteingroups_tab.tsv`: Abundance table after normalization, if chosen.
-    - `[contrast].proteus.raw_proteingroups_tab.tsv`: Abundance table without normalization.
+    - `[contrast]/[norm_function].normalized_proteingroups_tab.tsv`: Abundance table after normalization.
+    - `[contrast]/raw_proteingroups_tab.tsv`: Abundance table without normalization.
 
 </details>
 

nextflow.config

@@ -60,7 +60,7 @@ params {
 
     // Proteus-specific options
     proteus_measurecol_prefix = 'LFQ intensity '
-    proteus_norm_function    = 'normalizeMedian'
+    proteus_norm_function     = 'normalizeMedian'
     proteus_plotsd_method     = 'violin'
     proteus_plotmv_loess      =  true
     proteus_palette_name      = 'Set1'