fixed problem with pooled data dir

ParkerICI · Jul 23, 2018 · a82ea15 · a82ea15
1 parent f333552
commit a82ea15
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Showing 3 changed files with 14 additions and 12 deletions.
diff --git a/R/plot_data.R b/R/plot_data.R
@@ -128,12 +128,15 @@ load_clusters_data <- function(clusters, samples, dir.prefix, skip.missing = FAL
 #' 
 plot_clusters <- function(G, clusters, col.names, working.dir, plot.type, pool.clusters = FALSE, 
                           pool.samples = FALSE, samples.to.plot = NULL, facet.by = "Sample") {
-
+    if(!dir.exists(file.path(working.dir, "clusters_data")))
+        stop("clusters_data directory is missing, data cannot be plotted")
+
     cl.labels <- V(G)$Label[clusters]
     clusters.data <- NULL
 
-    if(is.null(V(G)$sample) && is.null(samples.to.plot)) { # Load the pooled data 
-        clusters.data <- load_rds_data(cl.labels, file.path(working.dir, "clusters_data", "pooled"))
+    if(is.null(V(G)$sample) && is.null(samples.to.plot)) { # Load the pooled data
+        pooled.data.dir <- tools::file_path_sans_ext(igraph::get.graph.attribute(G, "fname"))
+        clusters.data <- load_rds_data(cl.labels, file.path(working.dir, "clusters_data", "pooled", pooled.data.dir))
         clusters.data$sample <- NULL
     }
     else {

diff --git a/inst/shinyGUI/server/tab_graph.R b/inst/shinyGUI/server/tab_graph.R
@@ -68,15 +68,15 @@ fluidPage(
                    selectInput("graphui_node_size", "Nodes size", choices = c("Proportional", "Default"), width = "100%")
             ),
             column(6,
-                   numericInput("graphui_min_node_size", "Minimum node size", 2, min = 0, max = 1000)
+                   numericInput("graphui_min_node_size", "Minimum node size", 5, min = 0, max = 1000)
             )
         ),
         fluidRow(
             column(6,
-                   numericInput("graphui_max_node_size", "Maximum node size", 80, min = 0, max = 1000)
+                   numericInput("graphui_max_node_size", "Maximum node size", 60, min = 0, max = 1000)
             ),
             column(6,
-                   numericInput("graphui_landmark_node_size", "Landmark node size", 40, min = 0, max = 1000)
+                   numericInput("graphui_landmark_node_size", "Landmark node size", 20, min = 0, max = 1000)
             )
         ),
         fluidRow(
@@ -202,8 +202,7 @@ observe({
             updateSelectInput(session, "graphui_x_axis", choices = markers.for.plotting)
             updateSelectInput(session, "graphui_y_axis", choices = markers.for.plotting)
             sample.names <- panorama:::get_sample_names(G)
-            updateSelectInput(session, "graphui_active_sample", choices = c("All", sample.names),
-                                selected = input$graphui_active_sample)
+            updateSelectInput(session, "graphui_active_sample", choices = c("All", sample.names))
             updateSelectizeInput(session, "graphui_samples_to_plot", choices = sample.names)
             updateSelectInput(session, "graphui_stats_relative_to", choices = sample.names,
                                 selected = input$graphui_stats_relative_to)
@@ -366,10 +365,10 @@ output$graphui_plot = renderPlot(width = 1200, height = 800, expr = {
                             ))
                             return(p)
                         }
-                        else if(input$graphui_pool_samples_data) {
+                        else if(input$graphui_pool_samples_data && !input$graphui_pool_clusters_data) {
                             showModal(modalDialog(
                                 "This graph was derived from multiple independent clustering runs.",
-                                "Data from different samples cannot be pooled",
+                                "Data from different samples cannot be pooled, unless you also pool the clusters data",
                                 easyClose = TRUE
                             ))
                             return(p)
@@ -386,7 +385,7 @@ output$graphui_plot = renderPlot(width = 1200, height = 800, expr = {
                 }
                 else if(length(input$graphui_selected_nodes) > 0) {
                     session$sendCustomMessage(type = "plot_loading", "none")
-                    p <- panorama:::plot_clusters(G, 
+                    p <- panorama:::plot_clusters(G,
                                         clusters = get_selected_nodes(),
                                         col.names = markers.to.plot,
                                         working.dir = working.directory,

diff --git a/inst/shinyGUI/www/pixigraph.js b/inst/shinyGUI/www/pixigraph.js
@@ -122,7 +122,7 @@ class PixiGraph {
 
             if(d.type && d.type == "landmark") {
                 label.visible = true
-                fontSize = 24 
+                fontSize = 16 
             }
 
             label.style = {fontFamily: 'Arial', fontSize: fontSize, fill: 0x210E0F, align: 'left', strokeThickness: 1}