Merge pull request #226 from bigomics/fix-diffexpr-blinking

fix: diffexpr plots blink and initialize to all genes selected

components/board.expression/R/expression_plot_barplot.R

@@ -78,6 +78,7 @@ expression_plot_barplot_server <- function(id,
       showothers <- input$barplot_showothers
       sel <- sel()
       res <- res()
+      shiny::req(sel())
 
       psel <- rownames(res)[sel]
       gene <- pgx$genes[1, "gene_name"]

components/board.expression/R/expression_plot_maplot.R

@@ -75,7 +75,7 @@ expression_plot_maplot_server <- function(id,
       if (length(comp1) == 0) {
         return(NULL)
       }
-      shiny::req(pgx)
+      shiny::req(pgx, sel1())
 
       fdr <- as.numeric(gx_fdr())
       lfc <- as.numeric(gx_lfc())

components/board.expression/R/expression_plot_topfoldchange.R

@@ -58,6 +58,7 @@ expression_plot_topfoldchange_server <- function(id,
       comp <- comp() # input$gx_contrast
       sel <- sel()
       res <- res()
+      shiny::req(sel())
 
       psel <- rownames(res)[sel]
       gene <- pgx$genes[psel, "gene_name"]

components/board.expression/R/expression_plot_volcano.R

@@ -71,7 +71,6 @@ expression_plot_volcano_server <- function(id,
     plot_data <- shiny::reactive({
       # calculate required inputs for plotting
 
-
       comp1 <- comp1()
       fdr <- as.numeric(fdr())
       lfc <- as.numeric(lfc())
@@ -82,6 +81,8 @@ expression_plot_volcano_server <- function(id,
       sel2 <- sel2()
       df2 <- df2()
 
+      req(sel1())
+
       fam.genes <- res$gene_name
 
       if (is.null(res)) {
@@ -159,7 +160,7 @@ expression_plot_volcano_server <- function(id,
     })
 
 
-    plotly.RENDER <- function() {
+    plotly.RENDER <- reactive({
       pd <- plot_data()
       shiny::req(pd)
 
@@ -181,9 +182,9 @@ expression_plot_volcano_server <- function(id,
         showlegend = FALSE
       ) %>% plotly::layout(margin = list(b = 65))
       plt
-    }
+    })
 
-    modal_plotly.RENDER <- function() {
+    modal_plotly.RENDER <- reactive({
       fig <- plotly.RENDER() %>%
         plotly::layout(
           font = list(size = 18),
@@ -193,7 +194,7 @@ expression_plot_volcano_server <- function(id,
         )
       fig <- plotly::style(fig, marker.size = 20)
       fig
-    }
+    })
 
     PlotModuleServer(
       "pltmod",

components/board.expression/R/expression_server.R

@@ -80,10 +80,10 @@ ExpressionBoard <- function(id, pgx) {
     genetable_rows_selected <- reactiveVal()
 
     observe({
+      req(genetable$rows_selected())
       genetable_rows_selected(genetable$rows_selected())
     })
 
-
     # reactives ########
 
 
@@ -96,9 +96,6 @@ ExpressionBoard <- function(id, pgx) {
     })
 
 
-
-
-
     # functions #########
 
 
@@ -194,19 +191,18 @@ ExpressionBoard <- function(id, pgx) {
     }
 
     fullDiffExprTable <- shiny::reactive({
+      print('REACTIVE1 RUNNING')
       ## return the full DE table
       if (is.null(pgx)) {
         return(NULL)
       }
-      comp <- 1
-      tests <- "trend.limma"
-      fdr <- 1
-      lfc <- 0
       comp <- input$gx_contrast
       tests <- input$gx_statmethod
       fdr <- as.numeric(input$gx_fdr)
       lfc <- as.numeric(input$gx_lfc)
 
+      req(input$gx_contrast, input$gx_statmethod, input$gx_fdr, input$gx_lfc)
+
       if (is.null(comp)) {
         return(NULL)
       }