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

 Package: GSVA

-Version: 1.35.4

+Version: 1.35.5

 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"),

@@ -175,8 +175,7 @@ gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {

     generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf,

                             abs.ranking=as.logical(input$absRanking),

                             min.sz=input$minSz, max.sz=varMaxsz,

-                            ## parallel.sz=input$parallelSz, parallel.type=input$parallelType,

-                            parallel.sz=1, ## disable parallelism

+                            parallel.sz=1L, ## by now, disable parallelism

                             mx.diff=as.logical(input$mxDiff),

                             tau=selectedTau,

                             ssgsea.norm=as.logical(input$ssgseaNorm),

@@ -185,37 +184,26 @@ gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {

 }

 gsva_information <- function(input, output, session) {

-  if(class(generated_gsva) == "matrix")

-  {

-    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

-    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

-    output$result <- renderTable(resultInformation)

-    output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

-    tagList(

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

-      actionButton('closeSave','Save & Close')

-    )

-  }

+  gsva_es <- NA

+  if("matrix" %in% class(generated_gsva))

+    gsva_es <- as.data.frame(generated_gsva)

+  else if ("ExpressionSet" %in% class(generated_gsva))

+    gsva_es <- as.data.frame(exprs(generated_gsva))

+  else if ("SummarizedExperiment" %in% class(generated_gsva))

+    gsva_es <- as.data.frame(assays(generated_gsva)[[1]])

   else

-  {

-    

-    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

-    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

-    output$result <- renderTable(resultInformation)

-    if(class(generated_gsva) == "ExpressionSet") #If the generated gsva is an ExpressionSet

-    {

-      expressionSetObs <- exprs(generated_gsva)

-      output$plot <- renderPlot(multidensity(as.list(as.data.frame(expressionSetObs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2)) 

-    }

-    else

-    {

-      output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

-    }

-    tagList(

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

-      actionButton('closeSave','Save & Close')

-    )

-  }

+    stop("Unknown output generated by the call to the 'gsva()' function.")

+

+  resultInformation <- matrix(data = c(nrow(generated_gsva),

+                                       ncol(generated_gsva)),

+                                       nrow = 1, ncol = 2)

+  colnames(resultInformation) <- c("Nr. of gene sets", "Nr. of samples")

+  output$result <- renderTable(resultInformation)

+  output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2, cex.axis=1.2, cex.lab=1.5))

+  tagList(

+    downloadButton('downloadData', 'Download'),

+    actionButton('closeSave','Save & Close')

+  )

 }

 download_handler <- function(input, output, session) {

@@ -225,14 +213,14 @@ download_handler <- function(input, output, session) {

       paste("gsva_es-", Sys.Date(), ".csv", sep="")

     },

     content = function(file) {

-      if(class(generated_gsva) == "matrix") #If the whole object is a matrix

+      if("matrix" %in% class(generated_gsva)) # if the whole object is a matrix

       {

         dataFrameObs <- as.data.frame(generated_gsva)

         write.csv(dataFrameObs, file)

       }

       else

       {

-        if(class(generated_gsva) == "ExpressionSet") #If the generated gsva result value is an ExpressionSet

+        if("ExpressionSet" %in% class(generated_gsva)) #If the generated gsva result object is an ExpressionSet

         {

           expressionSetObs <- exprs(generated_gsva)

           dataFrameObs <- as.data.frame(expressionSetObs)

@@ -8,13 +8,13 @@ selectDataInput <- function(id) {

   #UI declaration

   column(

     3,

-    h3("Select data source:"),

+    h3("Data input:"),

     #Select data source

     wellPanel(fluidRow(

       column(

         12,

-        #Select matrix

-        radioButtons("matrixSourceType", "Select matrix:",

+        #Select expression data matrix

+        radioButtons("matrixSourceType", "Select expression data matrix:",

                      c("From file" = "fileMatrix",

                        "From workspace" = "varMatrix"))

         ,

@@ -37,7 +37,7 @@ selectDataInput <- function(id) {

         fluidRow(column(12,

                         HTML("<br>"))),

         #Select geneset

-        radioButtons("genesetSourceType", "Select GeneSet:",

+        radioButtons("genesetSourceType", "Select gene sets:",

                      c("From file" = "fileGeneset",

                        "From workspace" = "varGeneset"))

         ,

@@ -54,7 +54,7 @@ selectDataInput <- function(id) {

                       ls(envir=.GlobalEnv))

         ),

         HTML("<br>"),

-        radioButtons("arg", "Control arguments:",

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

                      c("No" = "no",

                        "Yes" = "yes"))

       )

@@ -69,7 +69,7 @@ mainDataInput <- function(id) {

   #UI Definition

   mainPanel(width = 6,

-            h2("Generated GSVA data:"),

+            ## h2("GSVA: gene set variation analysis"),

             textOutput("information"),

             plotOutput("plot"),

             tableOutput("result"),

@@ -85,7 +85,7 @@ argumentsDataInput <- function(id) {

     3,

     conditionalPanel(

       condition = "input.arg == 'yes'",

-      h3("Select arguments:"),

+      h3("Parameters:"),

       wellPanel(fluidRow(

         column(

           12,

@@ -98,9 +98,6 @@ argumentsDataInput <- function(id) {

                          "True" = TRUE)),

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

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

-          numericInput("parallelSz","parallel.sz:",value = 0),

-          selectInput("parallelType", "parallel.type:",

-                      c("SOCK","MPI","NWS")),

           radioButtons("mxDiff", "mx.diff:",

                        c("True" = TRUE,

                          "False" = FALSE)),

@@ -110,14 +107,11 @@ argumentsDataInput <- function(id) {

           ),

           conditionalPanel(

             condition = "input.method == 'ssgsea'",

-            numericInput("tau2","tau:",value = 0.25)

+            numericInput("tau2","tau:",value = 0.25),

+            radioButtons("ssgseaNorm", "ssgsea.norm:",

+                         c("True" = TRUE,

+                           "False" = FALSE)),

           ),

-          conditionalPanel(

-            condition = "input.method == 'zscore' || input.method == 'plage'"

-          ),

-          radioButtons("ssgseaNorm", "ssgsea.norm:",

-                       c("True" = TRUE,

-                         "False" = FALSE)),

           radioButtons("verbose", "verbose:",

                        c("True" = TRUE,

                          "False" = FALSE))

@@ -126,7 +120,14 @@ argumentsDataInput <- function(id) {

   )

 }

-fluidPage(theme = shinytheme("simplex"),	

+fluidPage(

+  theme = shinytheme("spacelab"),	

+  tags$head(

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

+  ),

+  titlePanel(div(h2("GSVA WebApp", align="left"),

+             tags$img(src="GSVA.png", align="center", height=75, width=75)),

+             windowTitle="GSVA"),

 	fluidRow(

 	  selectDataInput("dataInput"),

 	  mainDataInput("mainInput")

@@ -135,4 +136,4 @@ fluidPage(theme = shinytheme("simplex"),

 	    argumentsDataInput("argumentsInput")

 	  )

 	)

-)

\ No newline at end of file

+)

new file mode 100644

Binary files /dev/null and b/inst/shinyApp/www/GSVA.png differ

new file mode 100644

@@ -0,0 +1,5 @@

+.shiny-output-error-validation {

+	font-size: 16px;

+	font-weight: bold;

+	color: green;

+      }