From 5c233079ed4c30a9b416c6db9ceab76e11807359 Mon Sep 17 00:00:00 2001
From: csiu <celia.sy.siu@gmail.com>
Date: Sun, 16 Oct 2016 22:05:06 -0700
Subject: [PATCH] update format + remove trailing whitespace

---
 server.R | 54 +++++++++++++++++++++++++++++-------------------------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/server.R b/server.R
index 11c3f37..673705a 100644
--- a/server.R
+++ b/server.R
@@ -52,7 +52,7 @@ shinyServer(function(input, output, session) {
 
   #shows the button when first population selected in plot
   observe({
-    if((((is.null(selected_data()) | is.null(dim(selected_data()))) & !input$selectDefinedGroup) | 
+    if((((is.null(selected_data()) | is.null(dim(selected_data()))) & !input$selectDefinedGroup) |
        input$selectDefinedGroup & length(input$whichGroups)==0) | !is.null(rValues$selected_vector1)){
       disable("pop_one_selected")
     } else{
@@ -103,14 +103,14 @@ shinyServer(function(input, output, session) {
     show('histPlot')
     show("reload")
   })
-  
+
   #output$newPlot <- renderPlotly({
    # input$pop_selected
     #new_tsne <- isolate(selected_data())
     #plot_ly(new_tsne, x = ~x, y = ~y, text = ~key) %>%
      # layout(dragmode = "select")})
-  
-  
+
+
   # do I want to select defined groups?------
   observe({
     if(input$selectDefinedGroup){
@@ -137,7 +137,7 @@ shinyServer(function(input, output, session) {
       })
     }
   })
-  
+
   observe({
     if(input$pop_two_selected == 1){
       hide('div_select_two')
@@ -159,19 +159,19 @@ shinyServer(function(input, output, session) {
       })
     }
   })
-  
+
   second_clicked_eds <-reactive({input$pop_two_selected
     g1 = tsne[ tsne$barcode %in% barcodes$Barcode[isolate({rValues$selected_vector1})],]
     g2 = tsne[tsne$barcode %in% barcodes$Barcode[isolate({rValues$selected_vector2})],]
     list(g1, g2)})
-  
+
 
 
 
   second_clicked <-reactive({input$pop_two_selected})
-  
-  
-  
+
+
+
   # Once group 1 and group 2 of cells are selected,
   # create 10 boxplots showing the gene expression distributions
   # of group 1 and group 2 for the top 10 up-regulated and
@@ -179,11 +179,11 @@ shinyServer(function(input, output, session) {
   output$histPlot <- renderPlotly({
     if ( !is.null(differentiallyExpressed()) ) {
       gene_cnt <- 10
-      
+
       nbr_group1 <- sum(rValues$selected_vector1)
       nbr_group2 <- sum(rValues$selected_vector2)
       nbr_barcodes <- nbr_group1 + nbr_group2
-      
+
       diff_genes <- differentiallyExpressed()$`Gene Symbol`
       if(is.null(input$difGeneTable_rows_selected)){
       gene_idx <- c(1:gene_cnt, (length(diff_genes)-gene_cnt+1):length(diff_genes))
@@ -195,8 +195,8 @@ shinyServer(function(input, output, session) {
         gene_idx <- which(genes$Symbol == diff_genes[n])
         dat1 <- log2(expression[gene_idx, rValues$selected_vector1] + 0.1)
         dat2 <- log2(expression[gene_idx, rValues$selected_vector2] + 0.1)
-        
-        dg_mat <- rbind(dg_mat, 
+
+        dg_mat <- rbind(dg_mat,
                         data.frame(gene = diff_genes[n],
                                    expr = c(dat1, dat2),
                                    group = c(rep("1", nbr_group1),
@@ -205,20 +205,20 @@ shinyServer(function(input, output, session) {
                         )
         )
       }
-      
+
       # dg_mat %>% mutate(
       #   gene = as.factor(gene),
       #   expr = as.numeric(expr),
       #   group = as.factor(group),
       #   panel = as.factor(panel)) %>%
-      dg_mat <- 
+      dg_mat <-
         dg_mat %>% mutate(
           gene = as.character(gene),
           expr = as.numeric(expr),
           group = as.factor(group),
           panel = as.factor(panel)) %>%
         arrange(panel)
-      
+
       dg_mat$gene <- factor(dg_mat$gene, levels = dg_mat$gene)
       ggplot(dg_mat, aes(x=group, y=expr, fill=group)) +
         geom_boxplot() +
@@ -229,9 +229,9 @@ shinyServer(function(input, output, session) {
       plotly_empty()
     }
   })
-  
 
-  
+
+
   output$tSNE_summary <- renderPlotly({
     groups <- second_clicked_eds()
     g1 = groups[[1]]
@@ -239,12 +239,12 @@ shinyServer(function(input, output, session) {
     g1["group"] <- rep('group 1', dim(g1)[1])
     g2["group"] <- rep('group 2', dim(g2)[1])
     both_groups = rbind(g1, g2)
-    plot_ly(both_groups, x = ~tSNE_1, y = ~tSNE_2, text = ~barcode, color = ~group, colors = c("dark blue", "dark red"), 
+    plot_ly(both_groups, x = ~tSNE_1, y = ~tSNE_2, text = ~barcode, color = ~group, colors = c("dark blue", "dark red"),
             key = ~barcode, source = "selection_plot_two") %>%
                layout(dragmode = "select",xaxis = list(range = c(-40,40)),
                       yaxis = list(range = c(-40,40)))
     })
-  
+
   # histogram of cells -----------
   output$cell_type_summary <- renderPlotly({
     tsne_id <- table(tsne$id)
@@ -264,8 +264,8 @@ shinyServer(function(input, output, session) {
       add_trace(y=~g2_cell_counts, name = "group 2") %>%
       layout( yaxis = list(title = 'Count'), barmode = 'group')
   })
-    
-  
+
+
 
   output$downloadDifGenes = downloadHandler(
     filename = 'difGenes.tsv',
@@ -325,7 +325,7 @@ shinyServer(function(input, output, session) {
       enable('exprGeneButton')
     }
   })
-  
+
   geneExpr_genes <- reactive({
     # Take a dependency on input$goButton
     input$exprGeneButton
@@ -357,7 +357,11 @@ shinyServer(function(input, output, session) {
       output[[plotname]] <- renderPlotly({
         gene_of_interest <- parse_gene_input(geneExpr_genes()[my_i])
         gene_name <- parse_gene_input(geneExpr_genes()[my_i], get="name")
-        plot_geneExpr(gene_of_interest, gene_name, input_midplot=input$Midpoint, color_low = input$colmin, color_mid = input$colmid, color_high = input$colmax)
+        plot_geneExpr(gene_of_interest, gene_name,
+                      input_midplot=input$Midpoint,
+                      color_low = input$colmin,
+                      color_mid = input$colmid,
+                      color_high = input$colmax)
       })
     })
   }