Browse code

new css changes in dashboard

pablo-rodr-bio2 authored on 17/05/2021 17:29:04
Showing10 changed files

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@@ -1,9 +1,13 @@
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 Package: GSVA
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 <<<<<<< HEAD
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+<<<<<<< HEAD
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 Version: 1.39.31
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 =======
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 Version: 1.39.30
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 >>>>>>> beautifying UI
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+=======
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+Version: 1.39.32
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+>>>>>>> new css changes in dashboard
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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@@ -9,30 +9,28 @@ argumentsDataUI <- function(id) {
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       column(
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         width = 12,
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         align = "center",
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-        h4("Parameters", style="font-weight: bold")
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+        h4("PARAMETERS", style="font-weight: bold")
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       )
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     ),
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-    wellPanel(
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-      
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-      selectInput(ns("method"), "Choose method:",
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+    wellPanel( id= "args-well",
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+      selectInput(ns("method"), "Method",
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                   choices = methodChoices),
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-      selectInput(ns("kcdf"), "Choose kcdf:",
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+      selectInput(ns("kcdf"), "kcdf",
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                   c("Gaussian","Poisson","none")),
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       radioButtons(ns("absRanking"), "abs.ranking:",
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                    c("False" = FALSE,
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                      "True" = TRUE)),
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-      numericInput(ns("minSz"),"min.sz:", value = 1),
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-      numericInput(ns("maxSz"),"max.sz (Write 0 for infinite):", value = 0),
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-      radioButtons(ns("mxDiff"), "mx.diff:",
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+      numericInput(ns("minSz"),"min.sz", value = 1),
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+      numericInput(ns("maxSz"),"max.sz (Write 0 for infinite)", value = 0),
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+      radioButtons(ns("mxDiff"), "mx.diff",
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                    c("True" = TRUE,
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                      "False" = FALSE)),
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-      numericInput(ns("tau"),"tau:", value = 1),
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+      numericInput(ns("tau"),"tau", value = 1),
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       radioButtons(ns("ssgseaNorm"), "ssgsea.norm:",
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                    c("True" = TRUE,
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                      "False" = FALSE))
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     )
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   )
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-  
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 }
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 argumentsDataServer <- function(id){
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@@ -1,15 +1,8 @@
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 closeBtnUI <- function(id){
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   ns <- NS(id)
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-  hidden(actionButton(ns("closeSave"), "Save & Close", 
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+  hidden(actionButton(ns("closeSave"), "SAVE & CLOSE", 
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                       icon = icon("window-close"),
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-                      width = "10vw",
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-                      style = "color: #fff; 
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-                      background-color: red;
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-                      font-weight: bold;
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-                      border-color: #fff;
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-                      padding: 5px 5px 5px 5px;
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-                      margin: 6px 5px 6px 15px;"
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-                      ))
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+                      width = "10vw"))
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 }
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 closeBtnServer <- function(id, gs){
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@@ -1,14 +1,7 @@
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 downloadUI <- function(id) {
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   ns <- NS(id)
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   hidden(
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-    downloadButton(ns('downloadData'), 'Download',
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-                   style = "color: #fff;
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-                   background-color: #27ae60;
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-                   font-weight: bold;
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-                   border-color: #fff;
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-                   padding: 5px 14px 5px 14px;
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-                   margin: 6px 5px 6px 15px;
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-                   width: 10vw;")) 
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+    downloadButton(ns('downloadData'), 'DOWNLOAD')) 
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 }
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 downloadServer <- function(id, gs){
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@@ -1,8 +1,9 @@
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 geneSetsUI <- function(id){
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   ns <- NS(id)
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   div( id = ns("genesets-input"),
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-    radioButtons(ns("genesetSourceType"), "Select Gene Sets:",
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-                 c("From file" = "fileGeneset",
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+    radioButtons(ns("genesetSourceType"), 
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+                 label = h5("GENE SETS", style="font-weight: bold"),
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+                 choices = c("From file" = "fileGeneset",
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                    "From workspace" = "varGeneset")),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
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@@ -1,3 +1,4 @@
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+### LOADING LIBRARIES
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 library(shiny)
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 library(shinythemes)
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 library(plotly)
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@@ -11,7 +12,17 @@ library(promises)
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 library(shinyjs)
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 library(shinybusy)
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 library(shinydashboard)
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+
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+### there seems to be a problem with the DT package colliding with plotly
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+### so first check if the package is loaded and if it is, unload it
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+if("DT" %in% (.packages())) {
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+  detach("package:DT", unload=TRUE)
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+}
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+
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+### setting plan for futures
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 plan(multisession)
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+
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+### sourcing all modules
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 source("argumentsDataModule.R")
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 source("modalGSVAModule.R")
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 source("downloadModule.R")
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@@ -23,6 +34,7 @@ source("geneSetsModule.R")
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 source("argumentsDataModule.R")
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 source("closeModule.R")
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+### setting a global in "method" choices for gsva()
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 methodChoices <- c( "GSVA" = "gsva",
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                     "ssGSEA" = "ssgsea",
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                     "zscore" = "zscore",
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@@ -1,8 +1,9 @@
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 matrixUI <- function(id){
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   ns <- NS(id)
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   div(id = ns("matrix-input"),
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-    radioButtons(ns("matrixSourceType"), "Select Expression Data Matrix:",
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-                 c("From file" = "fileMatrix",
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+    radioButtons(ns("matrixSourceType"),
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+                 label = h5("EXPRESSION DATA MATRIX", style="font-weight: bold"),
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+                 choices = c("From file" = "fileMatrix",
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                    "From workspace" = "varMatrix")),
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     conditionalPanel(
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       condition = "input.matrixSourceType == 'fileMatrix'", ns = ns,
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@@ -200,7 +200,7 @@ function(input, output, session) {
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     resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),
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                                     "Nr of samples" = ncol(rv$gs))
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     resultInformation
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-  })
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+  }, bordered = TRUE)
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   # TEXT2
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   output$text2 <- renderUI({
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@@ -12,26 +12,21 @@ dashboardPage(
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     tags$head(
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       tags$link(rel = "stylesheet", type = "text/css", href = "style.css")
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     ),
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-    fluidRow(
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-      column(
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-        width = 12,
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-        align = "center",
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-        h3("Data Input", style="font-weight: bold")
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-      )
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-    ),
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-    # h3("Data input"),
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+    div(h3("DATA INPUT", style="font-weight: bold"), align = "center"),
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+    br(),
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     matrixUI("matrix1"),
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     br(),
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     geneSetsUI("genes1"),
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     br(),
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-    radioButtons("arg", "Change default settings?",
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+    radioButtons(inputId = "arg",
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+                 label = h5("CHANGE DEFAULT SETTINGS?", style="font-weight: bold"),
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                  c("No" = "no",
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                    "Yes" = "yes")),
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     br(),
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     fluidRow(
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       column(
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         width = 12, align = "left",
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-        actionButton("button", "Run", class = "run-btn", icon = icon("play-circle"),
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+        actionButton("button", "RUN", class = "run-btn", icon = icon("play-circle"),
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                      width = "10vw"),
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         downloadUI("download"),
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         closeBtnUI("close")
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@@ -1,6 +1,7 @@
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-#errorsGsva{color: red;
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-font-size: 20px;
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-font-weight: bold;
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+#errorsGsva {
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+  color: red;
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+  font-size: 20px;
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+  font-weight: bold;
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 }
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 #title_gsva {
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@@ -17,10 +18,46 @@ font-weight: bold;
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 #matrix1-matrix-input, #genes1-genesets-input {
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   background-color: #708090;
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+  border-radius: 15px;
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+  padding-bottom: 5px;
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+}
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+
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+#matrix1-matrixSourceType-label, #genes1-genesetSourceType-label {
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+  background-color: #6495ED;
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+  display: inline-block;
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+  text-align: center;
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+  width: 100%;
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+  border-radius: 15px;
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 }
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 #arg {
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-  background-color: #BC8F8F;
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+  background-color: #708090;
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+  border-radius: 15px;
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+	padding: 12px 15px 12px 15px;
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+}
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+
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+#args-well {
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+  background: #708090;
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+  color: white;
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+}
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+
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+#download-downloadData {
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+  color: #fff;
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+  background-color: #27ae60;
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+  font-weight: bold;
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+  border-color: #fff;
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+  padding: 5px 14px 5px 14px;
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+  margin: 6px 5px 6px 15px;
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+  width: 10vw;
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+}
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+
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+#close-closeSave{
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+  color: #fff;
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+  background-color: red;
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+  font-weight: bold;
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+  border-color: #fff;
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+  padding: 5px 5px 5px 5px;
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+  margin: 6px 5px 6px 15px;
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 }
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 .left-side, .main-sidebar {