Merge branch 'develop' into subplot-barplot-conversion-to-plotly

bigomics · Feb 24, 2023 · fdd8f00 · fdd8f00
2 parents 6baf303 + 3d9c21b
commit fdd8f00
Show file tree

Hide file tree

Showing 73 changed files with 3,909 additions and 2,190 deletions.
diff --git a/components/00SourceAll.R b/components/00SourceAll.R
@@ -71,6 +71,8 @@ if(!file.exists('00SourceAll.R')) {
   source('base/R/pgx-vizpanels.R',encoding='UTF-8')
   source('base/R/pgx-wordcloud.R',encoding='UTF-8')
   source('base/R/PlotModule.R',encoding='UTF-8')
+  source('base/R/TableModule.R',encoding='UTF-8')
+  source('base/R/TableModule2.R',encoding='UTF-8')
   source('base/R/ui-code.R',encoding='UTF-8')
   source('base/R/xcr-graph.r',encoding='UTF-8')
   source('base/R/xcr-math.r',encoding='UTF-8')
@@ -102,6 +104,8 @@ if(!file.exists('00SourceAll.R')) {
   source('board.connectivity/R/connectivity_plot_enrichmentGraph.R',encoding='UTF-8')
   source('board.connectivity/R/connectivity_plot_leadingEdgeGraph.R',encoding='UTF-8')
   source('board.connectivity/R/connectivity_server.R',encoding='UTF-8')
+  source('board.connectivity/R/connectivity_table_similarity_scores.R',encoding='UTF-8')
+  source('board.connectivity/R/connectivity_table_similarity_scores2.R',encoding='UTF-8')
   source('board.connectivity/R/connectivity_ui.R',encoding='UTF-8')
   source('board.correlation/R/correlation_plot_cor_graph.R',encoding='UTF-8')
   source('board.correlation/R/correlation_plot_partial_correlation.R',encoding='UTF-8')
@@ -162,8 +166,8 @@ if(!file.exists('00SourceAll.R')) {
   source('board.expression/R/expression_plot_volcanoAll.R',encoding='UTF-8')
   source('board.expression/R/expression_plot_volcanoMethods.R',encoding='UTF-8')
   source('board.expression/R/expression_server.R',encoding='UTF-8')
-  source('board.expression/R/expression_table_FDRtable.R',encoding='UTF-8')
   source('board.expression/R/expression_table_fctable.R',encoding='UTF-8')
+  source('board.expression/R/expression_table_FDRtable.R',encoding='UTF-8')
   source('board.expression/R/expression_table_genetable.R',encoding='UTF-8')
   source('board.expression/R/expression_table_gsettable.R',encoding='UTF-8')
   source('board.expression/R/expression_ui.R',encoding='UTF-8')
@@ -186,9 +190,9 @@ if(!file.exists('00SourceAll.R')) {
   source('board.intersection/R/intersection_plot_scatterplot_pairs.R',encoding='UTF-8')
   source('board.intersection/R/intersection_plot_table_venn_diagram.R',encoding='UTF-8')
   source('board.intersection/R/intersection_server.R',encoding='UTF-8')
-  source('board.intersection/R/intersection_table_venntable.R',encoding='UTF-8')
   source('board.intersection/R/intersection_ui.R',encoding='UTF-8')
   source('board.loading/R/loading_server.R',encoding='UTF-8')
+  source('board.loading/R/loading_table_datasets.R',encoding='UTF-8')
   source('board.loading/R/loading_tsneplot.R',encoding='UTF-8')
   source('board.loading/R/loading_ui.R',encoding='UTF-8')
   source('board.signature/R/signature_plot_enplots.R',encoding='UTF-8')
@@ -216,7 +220,21 @@ if(!file.exists('00SourceAll.R')) {
   source('board.upload/R/UploadModule.R',encoding='UTF-8')
   source('board.user/R/user_server.R',encoding='UTF-8')
   source('board.user/R/user_ui.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_correlation_network.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_eigengene_clustering.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_enrichment.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_gclustering.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_gdendogram.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_heatmap_membership.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_membership_v_trait.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_module_graph.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_module_membership.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_MTrelationships.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_s_independence.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_plot_TOMheatmap.R',encoding='UTF-8')
   source('board.wgcna/R/wgcna_server.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_table_enrichment.R',encoding='UTF-8')
+  source('board.wgcna/R/wgcna_table_genes.R',encoding='UTF-8')
   source('board.wgcna/R/wgcna_ui.R',encoding='UTF-8')
   source('board.wordcloud/R/wordcloud_plot_enrichment.R',encoding='UTF-8')
   source('board.wordcloud/R/wordcloud_plot_wordcloud.R',encoding='UTF-8')

diff --git a/components/app/R/global.R b/components/app/R/global.R
@@ -28,7 +28,20 @@ options(shiny.maxRequestSize = 999*1024^2)  ## max 999Mb upload
 options(shiny.fullstacktrace = TRUE)
 # The following DT global options ensure
     # 1. The header scrolls with the X scroll bar
-options(DT.options = list(autoWidth = FALSE, scrollX = TRUE))
+    # 2. The Y scroller works properly and no blank rows are displayed
+options(DT.options = list(
+  autoWidth = FALSE,
+  scrollX = TRUE,
+  fillContainer = FALSE
+))
+# Set global modal height values for tables.
+  # - The SCROLLY_MODAL defines the size of the scroll Y bar on the modals,
+  # this only defines the srollable part of the table, not the header height.
+  # - The TABLE_HEIGHT_MODAL defines the whole width of the table + header,
+  # this will define how close the caption is to the table.
+SCROLLY_MODAL <<- "55vh"
+TABLE_HEIGHT_MODAL <<- "75vh"
+
 reticulate::use_miniconda('r-reticulate')
 
 get_opg_root <- function() {