@@ -1,5 +1,5 @@

 Package: GSVA

-Version: 1.39.29

+Version: 1.39.30

 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"),

@@ -9,7 +9,7 @@ argumentsDataUI <- function(id) {

       column(

         width = 12,

         align = "center",

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

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

       )

     ),

     wellPanel(

@@ -2,10 +2,14 @@ closeBtnUI <- function(id){

   ns <- NS(id)

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

                       icon = icon("window-close"),

-                      style = "color: #fff;

-                      font-weight: bold;

+                      width = "10vw",

+                      style = "color: #fff; 

                       background-color: red;

-                      border-color: #fff;"))

+                      font-weight: bold;

+                      border-color: #fff;

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

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

+                      ))

 }

 closeBtnServer <- function(id, gs){

@@ -1,9 +1,14 @@

 downloadUI <- function(id) {

   ns <- NS(id)

-  hidden(downloadButton(ns('downloadData'), 'Download', style = "color: #fff;

-  font-weight: bold;

-  background-color: #27ae60;

-  border-color: #fff;" ))

+  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;")) 

 }

 downloadServer <- function(id, gs){

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

 geneSetsUI <- function(id){

   ns <- NS(id)

-  tagList(

-    radioButtons(ns("genesetSourceType"), "Select gene sets:",

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

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

                  c("From file" = "fileGeneset",

                    "From workspace" = "varGeneset")),

     conditionalPanel(

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

 matrixUI <- function(id){

   ns <- NS(id)

-  tagList(

-    radioButtons(ns("matrixSourceType"), "Select expression data matrix:",

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

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

                  c("From file" = "fileMatrix",

                    "From workspace" = "varMatrix")),

     conditionalPanel(

@@ -181,14 +181,17 @@ function(input, output, session) {

   # CLOSE BTN

   closeBtnServer("close", reactive(rv$gs))

-

+  

   # TEXT1

   output$text1 <- renderUI({

     req(rv$gs)

-    HTML(paste("<br/>", "\t To see the Empirical Cumulative Distribution Function 

-    of a Sample, click on its line in this plot and go

-      to the 'Gene.Set' Panel", "<br/>", sep="<br/>"))

+    tagList(

+      br(),

+      div("To see the Empirical Cumulative Distribution Function 

+      of a Sample, click on its line in this plot and go to the 

+      'Gene.Set' Panel", style="text-align: center;")

+    )

   })

   # TABLE

@@ -24,14 +24,15 @@ dashboardPage(

     br(),

     geneSetsUI("genes1"),

     br(),

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

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

                  c("No" = "no",

                    "Yes" = "yes")),

     br(),

     fluidRow(

       column(

         width = 12, align = "left",

-        actionButton("button", "Run"),

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

+                     width = "10vw"),

         downloadUI("download"),

         closeBtnUI("close")

       )

@@ -40,7 +41,7 @@ dashboardPage(

   dashboardBody(

     shinyjs::useShinyjs(),

-    add_busy_spinner(spin = "double-bounce", position = "bottom-right",

+    add_busy_spinner(spin = "cube-grid", position = "bottom-right",

                      height = "100px", width = "100px"),

     fluidRow(

       box(

@@ -50,7 +51,14 @@ dashboardPage(

                              textOutput("errorsGsva"),

                              htmlOutput("text1"),

                              plot1_UI("plot1"),

-                             tableOutput("result")

+                             br(),

+                             fluidRow(

+                               column(

+                                 width = 12,

+                                 align = "center",

+                                 tableOutput("result")

+                               )

+                             )

                     ),

                     tabPanel("GeneSets",

                              uiOutput("text2"),

@@ -15,6 +15,14 @@ font-weight: bold;

   margin: 5px 5px 5px 5px;

 }

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

+  background-color: #708090;

+}

+

+#arg {

+  background-color: #BC8F8F;

+}

+

 .left-side, .main-sidebar {

   padding-top: 75px;

 }

@@ -28,6 +36,15 @@ font-weight: bold;

 }

+.run-btn {

+  color: #fff; 

+  background-color: #6495ED;

+  font-weight: bold;

+  border-color: #fff;

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

+  margin: 5px 5px 5px 5px;

+}

+

 /**

 .main-header {