Svgoutput

program/shinyApp/R/enrichment_analysis/ui.R

@@ -48,7 +48,7 @@ geneset_panel_UI <- function(
           radioGroupButtons(
             inputId = ns("file_ext"),
             label = "File Type:",
-            choices = c(".png", ".tiff", ".pdf"),
+            choices = c(".png", ".tiff", ".pdf", ".svg"),
             selected = ".pdf"
           )
         ),

program/shinyApp/R/heatmap/server.R

@@ -360,15 +360,15 @@ heatmap_server <- function(id, data, params, updates){
             paste0(isolate(heatmap_reactives$customTitle), " ", Sys.time(), input$file_ext_Heatmap)
           },
           content = function(file){
-            save_pheatmap(heatmap_plot,filename=file,type=gsub("\\.","",input$file_ext_Heatmap))
+            save_pheatmap(res_tmp[[session$token]][["Heatmap"]]$plot,filename=file,type=gsub("\\.","",input$file_ext_Heatmap))
             on.exit({
               tmp_filename <- paste0(
                 getwd(),
                 file_path,
                 paste0(isolate(heatmap_reactives$customTitle), " ", Sys.time(), input$file_ext_Heatmap)
               )
               save_pheatmap(
-                heatmap_plot,
+                res_tmp[[session$token]][["Heatmap"]]$plot,
                 filename = tmp_filename,
                 type = gsub("\\.","",input$file_ext_Heatmap)
               )

program/shinyApp/R/heatmap/ui.R

@@ -114,8 +114,8 @@ heatmap_main <- function(ns){
       numericInput(
         inputId = ns("row_label_no"),
         label = "Threshold upon which explicit labels are shown",
-        min = 0, 
-        step = 1, 
+        min = 0,
+        step = 1,
         value = 25
       ),
       actionButton(
@@ -155,9 +155,9 @@ heatmap_main <- function(ns){
         style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
         NULL,
         radioGroupButtons(
-          inputId = ns("file_ext_Heatmap"), 
+          inputId = ns("file_ext_Heatmap"),
           label = "File Type:",
-          choices = c(".png", ".tiff", ".pdf"), 
+          choices = c(".png", ".tiff", ".pdf", ".svg"),
           selected = ".png"
         )
       ),

program/shinyApp/R/pca/ui.R

@@ -113,7 +113,7 @@ pca_main_panel <- function(ns){
             radioGroupButtons(
               inputId = ns("file_ext_plot1"),
               label = "File Type:",
-              choices = c(".png", ".tiff", ".pdf"),
+              choices = c(".png", ".tiff", ".pdf", ".svg"),
               selected = ".png"
             )
           ),
@@ -192,7 +192,7 @@ pca_main_panel <- function(ns){
             radioGroupButtons(
               inputId = ns("file_ext_Loadings"),
               label = "File Type:",
-              choices = c(".png", ".tiff", ".pdf"),
+              choices = c(".png", ".tiff", ".pdf", ".svg"),
               selected = ".png"
             )
           )
@@ -208,7 +208,7 @@ pca_main_panel <- function(ns){
           ),
           uiOutput(outputId = ns("EntitieAnno_Loadings_matrix_ui")),
           uiOutput(outputId = ns("nPCAs_to_look_at_ui")),
-  
+
           sliderInput(
             inputId = ns("filterValue"),
             label = "absolute Loading threshold to filter entities with low impact",
@@ -254,7 +254,7 @@ pca_main_panel <- function(ns){
             radioGroupButtons(
               inputId = ns("file_ext_Loadings_matrix"),
               label = "File Type:",
-              choices = c(".png", ".tiff", ".pdf"),
+              choices = c(".png", ".tiff", ".pdf", ".svg"),
               selected = ".png"
             )
           )
@@ -304,7 +304,7 @@ pca_main_panel <- function(ns){
             radioGroupButtons(
               inputId = ns("file_ext_Scree"),
               label = "File Type:",
-              choices = c(".png", ".tiff", ".pdf"),
+              choices = c(".png", ".tiff", ".pdf", ".svg"),
               selected = ".png"
             )
           )

program/shinyApp/R/pre_processing/ui.R

@@ -85,7 +85,7 @@ pre_processing_main_panel <- mainPanel(
       radioGroupButtons(
         inputId = "file_ext_Preprocess",
         label = "File Type:",
-        choices = c(".png", ".tiff", ".pdf"),
+        choices = c(".png", ".tiff", ".pdf", ".svg"),
         selected = ".png"
       )
     ),

program/shinyApp/R/sample_correlation/server.R

@@ -202,7 +202,7 @@ sample_correlation_server <- function(id, data, params){
 
       output$SavePlot_SampleCorrelation <- downloadHandler(
         filename = function() {
-          paste0(par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation, Sys.time(), input$file_ext_Heatmap)
+          paste0(par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation, Sys.time(), input$file_ext_SampleCorrelation)
         },
         content = function(file){
           save_pheatmap(par_tmp[[session$token]][["SampleCorr"]]$SampleCorrelationPlot_final,filename = file,type=gsub("\\.","",input$file_ext_SampleCorrelation))

program/shinyApp/R/sample_correlation/ui.R

@@ -67,9 +67,9 @@ sampleCorrelation_main_panel <- function(ns){
       style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
       NULL,
       radioGroupButtons(
-        inputId = ns("file_ext_SampleCorrelation"), 
+        inputId = ns("file_ext_SampleCorrelation"),
         label = "File Type:",
-        choices = c(".png", ".tiff", ".pdf"), 
+        choices = c(".png", ".tiff", ".pdf", ".svg"),
         selected = ".png"
       )
     ),

program/shinyApp/R/significance_analysis/ui.R

@@ -108,7 +108,7 @@ significance_analysis_main_ui <- function(ns){
             radioGroupButtons(
               inputId = ns("file_ext_Sig"),
               label = "File Type:",
-              choices = c(".png", ".tiff", ".pdf"),
+              choices = c(".png", ".tiff", ".pdf", ".svg"),
               selected = ".png"
             )
           ),

program/shinyApp/R/single_gene_visualisation/ui.R

@@ -69,7 +69,7 @@ single_gene_visualisation_main_ui <- function(ns){
         radioGroupButtons(
           inputId = ns("file_ext_singleGene"),
           label = "File Type:",
-          choices = c(".png", ".tiff", ".pdf"),
+          choices = c(".png", ".tiff", ".pdf", ".svg"),
           selected = ".png"
         )
       ),

program/shinyApp/ui.R

@@ -45,7 +45,7 @@ library(gridExtra)
 library(sva)
 library(pcaPP) # requires gfortran. Not sure how to install on server
 library(reshape2)
-# library(svglite)
+library(svglite)
 
 source("R/C.R")
 source("R/module_DownloadReport.R",local=T)