deseqTable

internals.R

@@ -84,7 +84,7 @@ beautifulTable <- function(data)  {
     filter = "top",
     extensions = c("Buttons", "ColReorder", "FixedColumns"),
     options = list(
-      dom = "lBtip",
+      dom = "Btlip",
       pageLength = 10,
       lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
       buttons = list(

panels/deseq-server.R

@@ -189,6 +189,32 @@ observeEvent(input$deseq_output_code,
              }
 )
 
-# output$deseqTable <- metaRender2(renderTable, {
-# }
-# )
+output$deseqTable <- renderDT({
+  validate(
+    need(physeq(), "Requires an abundance dataset"),
+    need(class(get_variable(physeq(), input$deseqContrastVar)) == "numeric" || 
+           length(input$deseqContrastMod) == 2, "Requires a continuous design or a selection of two modalities for a discrete design."),
+    need(results(), "Invalid input.")
+  )
+  
+  results() %>%
+    filter(padj <= 0.05) %>% ## Only significant OTUs
+    datatable(rownames = FALSE,
+              filter = "top",
+              extensions = c("Buttons", "ColReorder", "FixedColumns"),
+              options = list(dom = "Btlip",
+                             pageLength = 10,
+                             lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
+                             buttons = list('colvis',
+                                            list(extend = 'collection',
+                                                 buttons = c('copy', 'csv', 'excel', 'pdf'),
+                                                 text = 'Download')),
+                             colReorder = TRUE,
+                             scrollX = TRUE,
+                             fixedColumns = list(leftColumns = 1, rightColumns = 0)
+                             ),
+              width = "auto",
+              height = "auto") %>%
+    formatSignif(columns = c("baseMean", "log2FoldChange", "lfcSE", "stat", "padj", "pvalue"), digits = 4) %>%
+    formatStyle(columns = "log2FoldChange", color = DT::styleInterval(0, c('red', 'green')))
+  })
\ No newline at end of file

panels/deseq-ui.R

 deseq <- fluidPage(outputCodeButton(withLoader(plotOutput("deseq", height = 700))),
-                   #table
+                   box(
+                     title = "Table of OTUs with significant effect",
+                     width = NULL,
+                     status = "primary",
+                     collapsible = TRUE,
+                     collapsed = TRUE,
+                     DT::DTOutput("deseqTable")),
                    uiOutput("deseqUI"))