From 39752fb45a58950236e4ebd124c90792f6623304 Mon Sep 17 00:00:00 2001
From: Federico Marini <marinif@uni-mainz.de>
Date: Thu, 30 Jul 2020 11:36:28 +0200
Subject: [PATCH 1/5] R1-point2: Sorting the columns of the preview table
 aphabetically

---
 app.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/app.R b/app.R
index 98251c1..a95e4f6 100644
--- a/app.R
+++ b/app.R
@@ -40,6 +40,9 @@ createLinkGO <- function(val) {
 message("Loading R data...")
 load("trendseq.RData")
 
+# sorting columns for KDmat?
+KDmat <- KDmat[, order(colnames(KDmat))]
+
 # these objects needed to be updated in newer Bioc versions
 # txBygene <- updateObject(txBygene,verbose = FALSE)
 utrs <- updateObject(utrs, verbose = FALSE)

From 69d5e160f909e872d1d821e245da582692508cd4 Mon Sep 17 00:00:00 2001
From: Federico Marini <marinif@uni-mainz.de>
Date: Thu, 30 Jul 2020 11:37:20 +0200
Subject: [PATCH 2/5] R1-point1: Fixing the column with gene names to be always
 viewed even while scrolling

---
 app.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app.R b/app.R
index a95e4f6..b18b1c2 100644
--- a/app.R
+++ b/app.R
@@ -716,7 +716,7 @@ server <- function(input, output, session) {
           scrollY = 407,
           scroller = TRUE,
           pageLength = 50,
-          fixedColumns = FALSE
+          fixedColumns = TRUE
         )
       ) %>%
         formatRound(colnames(table), digits = 3) %>%

From f85c25bdca67f55e29e15608b2fb2f6d386bdb06 Mon Sep 17 00:00:00 2001
From: Federico Marini <marinif@uni-mainz.de>
Date: Thu, 30 Jul 2020 11:38:18 +0200
Subject: [PATCH 3/5] R1-point3: Adding copy/print/download buttons for the
 generated tables

---
 app.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/app.R b/app.R
index b18b1c2..fe879a4 100644
--- a/app.R
+++ b/app.R
@@ -928,12 +928,21 @@ server <- function(input, output, session) {
       paste0(colnames(table), "_kd")
     DT::datatable(
       table,
+      extensions = "Buttons",
       colnames = c("Gene" = 1),
       options = list(
         scrollX = TRUE,
         # scrollY = 300,
         searching = TRUE,
-        paging = FALSE
+        paging = FALSE,
+        dom = 'Bfrtip',
+        buttons = 
+          list('copy', 'print', list(
+            extend = 'collection',
+            buttons = c('csv', 'excel', 'pdf'),
+            text = 'Download'
+          )
+        )
       )
     ) %>%
       formatStyle("Gene",
@@ -956,13 +965,21 @@ server <- function(input, output, session) {
       kdtable,
       colnames = c("Gene" = 1),
       selection = "single",
-      extensions = c("FixedColumns"),
+      extensions = c("FixedColumns", "Buttons"),
       options = list(
         scrollX = TRUE,
         scrollY = 480,
         paging = FALSE,
         searching = TRUE,
-        fixedColumns = FALSE
+        fixedColumns = FALSE,
+        dom = 'Bfrtip',
+        buttons = 
+          list('copy', 'print', list(
+            extend = 'collection',
+            buttons = c('csv', 'excel', 'pdf'),
+            text = 'Download'
+          )
+        )
       )
     ) %>%
       formatStyle("Gene",

From f858d9e73924926aafbae2ce8bb5c4890009ba67 Mon Sep 17 00:00:00 2001
From: Federico Marini <marinif@uni-mainz.de>
Date: Thu, 6 Aug 2020 14:05:52 +0200
Subject: [PATCH 4/5] failsafe when no term is strictly detected as enriched

---
 app.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app.R b/app.R
index fe879a4..a788ee9 100644
--- a/app.R
+++ b/app.R
@@ -1037,7 +1037,13 @@ server <- function(input, output, session) {
   
   output$emap_ui <- renderUI({
     if(!(nrow(createGoenrich()) > 0))
-      return(NULL)
+      return(
+        tagList(
+          shiny::tags$br(),
+          shiny::tags$br(),
+          p(shiny::tags$em("You can not generate an enrichment map, no functional category has an adjusted p-value below 0.05..."))
+        )
+      )
     tagList(
       numericInput("emap_ngs", 
                    width = "25%",

From 00ed4d052fa866b145a117ab9ff0f19b1cb7af6a Mon Sep 17 00:00:00 2001
From: Federico Marini <marinif@uni-mainz.de>
Date: Thu, 6 Aug 2020 16:52:53 +0200
Subject: [PATCH 5/5] Button added also for the enrichment table

---
 app.R | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/app.R b/app.R
index a788ee9..45d2995 100644
--- a/app.R
+++ b/app.R
@@ -40,7 +40,7 @@ createLinkGO <- function(val) {
 message("Loading R data...")
 load("trendseq.RData")
 
-# sorting columns for KDmat?
+# sorting columns for KDmat
 KDmat <- KDmat[, order(colnames(KDmat))]
 
 # these objects needed to be updated in newer Bioc versions
@@ -1014,12 +1014,22 @@ server <- function(input, output, session) {
         ),
         rownames = FALSE,
         selection = "single",
-        extensions = c("FixedColumns"),
+        extensions = c("FixedColumns", "Buttons"),
         options = list(
           bInfo = 0,
           scrollX = TRUE,
+          scrollY = 480,
           fixedColumns = FALSE,
-          order = list(5, "asc")
+          paging = FALSE,
+          order = list(5, "asc"),
+          dom = 'Bfrtip',
+          buttons = 
+            list('copy', 'print', list(
+              extend = 'collection',
+              buttons = c('csv', 'excel', 'pdf'),
+              text = 'Download'
+            )
+          )
         ),
         escape = FALSE
       ) %>%