Make it so that boxplot of gene expression is possible #19

hackseq · Oct 17, 2016 · e8d6e3e · e8d6e3e
1 parent 85c7d0b
commit e8d6e3e
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Showing 3 changed files with 44 additions and 4 deletions.
diff --git a/global.R b/global.R
@@ -1,5 +1,6 @@
 library(readr)
 library(dplyr)
+library(tidyr)
 library(Matrix)
 library(plotly)
 library(magrittr)
@@ -81,3 +82,35 @@ plot_geneExpr <- function(gene_of_interest, gene_name,
     ggtitle(gene_name)
   ggplotly()
 }
+
+#' Draw geneExpr boxplot by cluster
+plot_geneExprGeneCluster <- function(gene_of_interest, gene_name){
+  the_genes <- setNames(gene_name, gene_of_interest)
+
+  gene_expr <-
+    expression[names(the_genes),] %>%
+    as.matrix() %>%
+    t() %>%
+    as.data.frame() %>%
+    tibble::rownames_to_column("barcode")
+  tsne1 <-
+    left_join(tsne, gene_expr, by="barcode") %>%
+    gather(gene, expr, starts_with("ENSG")) %>%
+    mutate(
+      gene = as.factor(gene),
+      gene = plyr::revalue(gene, the_genes)
+    )
+  tsne1 %>%
+    ggplot(aes(x=id, y=expr)) +
+    geom_boxplot() +
+    facet_wrap(~gene) +
+    xlab("Cluster") +
+    ylab("Normalized expression") +
+    theme_classic() +
+    theme(
+      axis.text.x = element_text(angle=90, hjust=1, vjust=0.5),
+      strip.background = element_rect(fill = NA, colour = NA)
+    )
+  ggplotly()
+}
+
diff --git a/server.R b/server.R
@@ -190,7 +190,7 @@ shinyServer(function(input, output, session) {
       } else{
         gene_idx = input$difGeneTable_rows_selected
       }
-      
+
       dg_mat <- c()
       for ( n in gene_idx ) {
         gene_idx <- which(genes$Symbol == diff_genes[n])
@@ -216,8 +216,8 @@ shinyServer(function(input, output, session) {
         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() + 
-        facet_wrap(~gene, scales="free_x", nrow=2, ncol=gene_cnt) + 
+      ggplot(dg_mat, aes(x=group, y=expr, fill=group)) + geom_boxplot() +
+        facet_wrap(~gene, scales="free_x", nrow=2, ncol=gene_cnt) +
         theme(panel.margin = unit(1, "lines"),
               panel.background = element_rect(fill = "white"),
               strip.background = element_rect(fill = "white"),
@@ -365,5 +365,12 @@ shinyServer(function(input, output, session) {
     })
   }
 
+  output$geneExprGeneCluster <- renderPlotly({
+    gene_of_interest <- parse_gene_input(geneExpr_genes())
+    gene_name <- parse_gene_input(geneExpr_genes(), get="name")
+    plot_geneExprGeneCluster(gene_of_interest, gene_name)
+  })
+
+
 }
 )
diff --git a/ui.R b/ui.R
@@ -58,7 +58,7 @@ shinyUI(
                                           )
 
                                ),
-                        column(8, uiOutput("geneExprPlot"))
+                        column(8, uiOutput("geneExprPlot"), plotlyOutput("geneExprGeneCluster"))
                ),
                # exploration of selection
                tabPanel( 'Compare',