fix: use pgx geneset genes

bigomics · May 9, 2024 · fb8a420 · fb8a420
1 parent 41c0209
commit fb8a420
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/components/board.enrichment/R/enrichment_plot_volcano.R b/components/board.enrichment/R/enrichment_plot_volcano.R
@@ -35,6 +35,7 @@ enrichment_plot_volcano_server <- function(id,
                                            gs_fdr,
                                            gs_lfc,
                                            subplot.MAR,
+                                           geneDetails,
                                            watermark = FALSE) {
   moduleServer(id, function(input, output, session) {
     volcano.RENDER <- shiny::reactive({
@@ -63,9 +64,7 @@ enrichment_plot_volcano_server <- function(id,
         text(0.5, 0.5, "Please select a geneset", col = "grey50")
         return()
       }
-      gs <- gs[1]
-
-      gset <- playdata::getGSETS(gs)[[1]]
+      gset <- geneDetails()$feature
       jj <- match(toupper(gset), toupper(limma$gene_name))
       sel.genes <- setdiff(limma$gene_name[jj], c(NA, "", " "))
 

diff --git a/components/board.enrichment/R/enrichment_server.R b/components/board.enrichment/R/enrichment_server.R
@@ -468,6 +468,7 @@ EnrichmentBoard <- function(id, pgx, selected_gxmethods = reactive(colnames(pgx$
       gs_fdr = shiny::reactive(input$gs_fdr),
       gs_lfc = shiny::reactive(input$gs_lfc),
       subplot.MAR = subplot.MAR,
+      geneDetails = geneDetails,
       watermark = WATERMARK
     )