@@ -1,9 +1,13 @@

 Package: GSVA

 <<<<<<< HEAD

+<<<<<<< HEAD

 Version: 1.39.31

 =======

 Version: 1.39.30

 >>>>>>> beautifying UI

+=======

+Version: 1.39.32

+>>>>>>> new css changes in dashboard

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),

              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),

@@ -9,30 +9,28 @@ argumentsDataUI <- function(id) {

       column(

         width = 12,

         align = "center",

-        h4("Parameters", style="font-weight: bold")

+        h4("PARAMETERS", style="font-weight: bold")

       )

     ),

-    wellPanel(

-      

-      selectInput(ns("method"), "Choose method:",

+    wellPanel( id= "args-well",

+      selectInput(ns("method"), "Method",

                   choices = methodChoices),

-      selectInput(ns("kcdf"), "Choose kcdf:",

+      selectInput(ns("kcdf"), "kcdf",

                   c("Gaussian","Poisson","none")),

       radioButtons(ns("absRanking"), "abs.ranking:",

                    c("False" = FALSE,

                      "True" = TRUE)),

-      numericInput(ns("minSz"),"min.sz:", value = 1),

-      numericInput(ns("maxSz"),"max.sz (Write 0 for infinite):", value = 0),

-      radioButtons(ns("mxDiff"), "mx.diff:",

+      numericInput(ns("minSz"),"min.sz", value = 1),

+      numericInput(ns("maxSz"),"max.sz (Write 0 for infinite)", value = 0),

+      radioButtons(ns("mxDiff"), "mx.diff",

                    c("True" = TRUE,

                      "False" = FALSE)),

-      numericInput(ns("tau"),"tau:", value = 1),

+      numericInput(ns("tau"),"tau", value = 1),

       radioButtons(ns("ssgseaNorm"), "ssgsea.norm:",

                    c("True" = TRUE,

                      "False" = FALSE))

     )

   )

-  

 }

 argumentsDataServer <- function(id){

@@ -1,15 +1,8 @@

 closeBtnUI <- function(id){

   ns <- NS(id)

-  hidden(actionButton(ns("closeSave"), "Save & Close", 

+  hidden(actionButton(ns("closeSave"), "SAVE & CLOSE", 

                       icon = icon("window-close"),

-                      width = "10vw",

-                      style = "color: #fff; 

-                      background-color: red;

-                      font-weight: bold;

-                      border-color: #fff;

-                      padding: 5px 5px 5px 5px;

-                      margin: 6px 5px 6px 15px;"

-                      ))

+                      width = "10vw"))

 }

 closeBtnServer <- function(id, gs){

@@ -1,14 +1,7 @@

 downloadUI <- function(id) {

   ns <- NS(id)

   hidden(

-    downloadButton(ns('downloadData'), 'Download',

-                   style = "color: #fff;

-                   background-color: #27ae60;

-                   font-weight: bold;

-                   border-color: #fff;

-                   padding: 5px 14px 5px 14px;

-                   margin: 6px 5px 6px 15px;

-                   width: 10vw;")) 

+    downloadButton(ns('downloadData'), 'DOWNLOAD')) 

 }

 downloadServer <- function(id, gs){

@@ -1,8 +1,9 @@

 geneSetsUI <- function(id){

   ns <- NS(id)

   div( id = ns("genesets-input"),

-    radioButtons(ns("genesetSourceType"), "Select Gene Sets:",

-                 c("From file" = "fileGeneset",

+    radioButtons(ns("genesetSourceType"), 

+                 label = h5("GENE SETS", style="font-weight: bold"),

+                 choices = c("From file" = "fileGeneset",

                    "From workspace" = "varGeneset")),

     conditionalPanel(

       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,

@@ -1,3 +1,4 @@

+### LOADING LIBRARIES

 library(shiny)

 library(shinythemes)

 library(plotly)

@@ -11,7 +12,17 @@ library(promises)

 library(shinyjs)

 library(shinybusy)

 library(shinydashboard)

+

+### there seems to be a problem with the DT package colliding with plotly

+### so first check if the package is loaded and if it is, unload it

+if("DT" %in% (.packages())) {

+  detach("package:DT", unload=TRUE)

+}

+

+### setting plan for futures

 plan(multisession)

+

+### sourcing all modules

 source("argumentsDataModule.R")

 source("modalGSVAModule.R")

 source("downloadModule.R")

@@ -23,6 +34,7 @@ source("geneSetsModule.R")

 source("argumentsDataModule.R")

 source("closeModule.R")

+### setting a global in "method" choices for gsva()

 methodChoices <- c( "GSVA" = "gsva",

                     "ssGSEA" = "ssgsea",

                     "zscore" = "zscore",

@@ -1,8 +1,9 @@

 matrixUI <- function(id){

   ns <- NS(id)

   div(id = ns("matrix-input"),

-    radioButtons(ns("matrixSourceType"), "Select Expression Data Matrix:",

-                 c("From file" = "fileMatrix",

+    radioButtons(ns("matrixSourceType"),

+                 label = h5("EXPRESSION DATA MATRIX", style="font-weight: bold"),

+                 choices = c("From file" = "fileMatrix",

                    "From workspace" = "varMatrix")),

     conditionalPanel(

       condition = "input.matrixSourceType == 'fileMatrix'", ns = ns,

@@ -200,7 +200,7 @@ function(input, output, session) {

     resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),

                                     "Nr of samples" = ncol(rv$gs))

     resultInformation

-  })

+  }, bordered = TRUE)

   # TEXT2

   output$text2 <- renderUI({

@@ -12,26 +12,21 @@ dashboardPage(

     tags$head(

       tags$link(rel = "stylesheet", type = "text/css", href = "style.css")

     ),

-    fluidRow(

-      column(

-        width = 12,

-        align = "center",

-        h3("Data Input", style="font-weight: bold")

-      )

-    ),

-    # h3("Data input"),

+    div(h3("DATA INPUT", style="font-weight: bold"), align = "center"),

+    br(),

     matrixUI("matrix1"),

     br(),

     geneSetsUI("genes1"),

     br(),

-    radioButtons("arg", "Change default settings?",

+    radioButtons(inputId = "arg",

+                 label = h5("CHANGE DEFAULT SETTINGS?", style="font-weight: bold"),

                  c("No" = "no",

                    "Yes" = "yes")),

     br(),

     fluidRow(

       column(

         width = 12, align = "left",

-        actionButton("button", "Run", class = "run-btn", icon = icon("play-circle"),

+        actionButton("button", "RUN", class = "run-btn", icon = icon("play-circle"),

                      width = "10vw"),

         downloadUI("download"),

         closeBtnUI("close")

@@ -1,6 +1,7 @@

-#errorsGsva{color: red;

-font-size: 20px;

-font-weight: bold;

+#errorsGsva {

+  color: red;

+  font-size: 20px;

+  font-weight: bold;

 }

 #title_gsva {

@@ -17,10 +18,46 @@ font-weight: bold;

 #matrix1-matrix-input, #genes1-genesets-input {

   background-color: #708090;

+  border-radius: 15px;

+  padding-bottom: 5px;

+}

+

+#matrix1-matrixSourceType-label, #genes1-genesetSourceType-label {

+  background-color: #6495ED;

+  display: inline-block;

+  text-align: center;

+  width: 100%;

+  border-radius: 15px;

 }

 #arg {

-  background-color: #BC8F8F;

+  background-color: #708090;

+  border-radius: 15px;

+	padding: 12px 15px 12px 15px;

+}

+

+#args-well {

+  background: #708090;

+  color: white;

+}

+

+#download-downloadData {

+  color: #fff;

+  background-color: #27ae60;

+  font-weight: bold;

+  border-color: #fff;

+  padding: 5px 14px 5px 14px;

+  margin: 6px 5px 6px 15px;

+  width: 10vw;

+}

+

+#close-closeSave{

+  color: #fff;

+  background-color: red;

+  font-weight: bold;

+  border-color: #fff;

+  padding: 5px 5px 5px 5px;

+  margin: 6px 5px 6px 15px;

 }

 .left-side, .main-sidebar {