Merge pull request #8 from mariavica/patch-devel

Patch devel
mariavica · Sep 21, 2017 · 8353b09 · 8353b09
2 parents 3aa217a + 1bafa2d
commit 8353b09
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Showing 3 changed files with 30 additions and 36 deletions.
diff --git a/rsconnect/shinyapps.io/mariavica/mirtools.dcf b/rsconnect/shinyapps.io/mariavica/mirtools.dcf
@@ -3,8 +3,8 @@ title: mirtools
 account: mariavica
 server: shinyapps.io
 appId: 181686
-bundleId: 889946
+bundleId: 890285
 url: https://mariavica.shinyapps.io/mirtools/
-when: 1499076352.40474
+when: 1499096979.51419
 asMultiple: FALSE
 asStatic: FALSE
diff --git a/server.r b/server.r
@@ -22,7 +22,6 @@ shinyServer(function(input, output) {
 
         uploadedm<-read.csv(inFile$datapath)
 
-
         mymirnas<-unlist(strsplit(as.character(uploadedm[,1]),c("\\,|\\ |\\\n")))
       }
 
@@ -31,12 +30,7 @@ shinyServer(function(input, output) {
         mymirnas<-unlist(strsplit(as.character(input$mirname),c("\\,|\\ |\\\n")))
       }
 
-
-            if (input$species!="select") {
-        specie<-which(species_name %in% input$species)
-        mymirnas<-paste(prefix[specie],mymirnas,sep="")
-        mymirnas<-gsub(paste(prefix[specie],prefix[specie],sep=""),prefix[specie],mymirnas)
-      } 
+
 
       if (input$capitalise) {
         mymirnas<-gsub("[mM][iI][rR]","miR",mymirnas)
@@ -53,8 +47,17 @@ shinyServer(function(input, output) {
         mymirnas<-gsub("J","j",mymirnas)
       }
 
+
+      if (input$species!="select") {
+        specie<-which(species_name %in% input$species)
+        sel<-c(grep("^miR",mymirnas),grep("^let",mymirnas))
+        mymirnas[sel]<-paste(prefix[specie],mymirnas[sel],sep="")
+        mymirnas[sel]<-gsub(paste(prefix[specie],prefix[specie],sep=""),prefix[specie],mymirnas[sel])
+      } 
+
+
       mymirnas<-mymirnas[which(mymirnas!="")]
-      print(mymirnas)
+      #print(mymirnas)
 
       a<-apply(versions.mirnas,2,perc,mymirnas)
 
@@ -70,23 +73,21 @@ shinyServer(function(input, output) {
       dat$x<-relevel(dat$x,"7.1")
       dat$x<-relevel(dat$x,"7.0")
       dat$x<-relevel(dat$x,"6.0")
-      print(dat)
+      #print(dat)
 
       maxs<-which(dat$y==max(dat$y))
       proposedversion<-dat[maxs[length(maxs)] ,"x"]	
 
 
       if (input$mirfrom != "I don't know") {
-        print("entering")
         selectedversion<-input$mirfrom
       } else {
         selectedversion<-proposedversion
       }
 
-      print(paste("miRBase_",selectedversion,sep=""))
+      #print(paste("miRBase_",selectedversion,sep=""))
 
       mymirnas<-as.character(mymirnas)
-
       mytrans<-data.frame(mymirnas)
 
       for (i in 1:nrow(mytrans)) {
@@ -99,9 +100,9 @@ shinyServer(function(input, output) {
 
             if (input$forceTranslation) {
                   coincidences <- which(t(versions.mirnas)==mymirnas[i])
-                  print(coincidences)
+                  #print(coincidences)
                   rowmir <- ceiling(coincidences[length(coincidences)]/(totcol-1))
-                  print(rowmir)
+                  #print(rowmir)
 
                   mytrans[i,2]<-as.character(versions.mirnas[rowmir, c(paste("miRBase_",as.character(input$mirto),sep="")) ])
             }
@@ -132,18 +133,15 @@ shinyServer(function(input, output) {
       paste("Most of your miRNAs are from version:",maketable()[[2]],"\n")
     })  
 
-
     output$percent <- renderPlot({
       datp<-maketable()[[3]]
       qplot(x=datp$x, y=datp$y, fill=datp$x) + geom_bar(stat="identity") +
         guides(fill=FALSE) + xlab("miRBase version") + ylab("Coincidence (%)")
-
     })
-
 
     output$translated<-renderTable(maketable()[[1]])
 
-    output$downloadTranslated <- downloadHandler( filename="translated.csv", content=function (file){ write.csv(maketable()[[1]], file, row.names=FALSE, sep="\t", quote=FALSE) })
+    output$downloadTranslated <- downloadHandler( filename="translated.csv", content=function (file){ write.table(maketable()[[1]], file, row.names=FALSE, sep="\t", quote=FALSE) })
 
 
 

diff --git a/ui.r b/ui.r
@@ -5,7 +5,7 @@ shinyUI(fluidPage(
     sidebarPanel(
 
       helpText("Upload your file (\"*txt\" or \"*csv\" plain file):"),
-      
+
       fileInput(inputId="csvfile", label=NULL , multiple = FALSE, accept = c(
         "text/csv", "text/comma-separated-values,text/plain",".csv",".txt"), width = NULL,
         buttonLabel = "Browse...", placeholder = "No file selected"),
@@ -26,36 +26,32 @@ shinyUI(fluidPage(
                   selected = "21", multiple = FALSE, selectize = TRUE, width = NULL, size = NULL),
 
    helpText(strong("Proofreading:")),
-
-
-
-        checkboxInput(inputId="forceTranslation",label="Force translation (miRNAs from other versions will be automatically translated to desired version)", value=FALSE),
 
-  checkboxInput(inputId="capitalise",label="Correct capital letters (valid only for \"miR\" and \"let\")", value=FALSE),
-  
-    
+   checkboxInput(inputId="forceTranslation",label="Force translation (miRNAs from other versions will be automatically translated to desired version)", value=FALSE),
+
+
   helpText("MiRNA species"),
 
   selectInput(inputId = "species", label=NULL, choices=c("select","Homo sapiens","Mus musculus"),
-              selected = "Specified in name", multiple = FALSE, selectize = TRUE, width = NULL, size = NULL)
+              selected = "Specified in name", multiple = FALSE, selectize = TRUE, width = NULL, size = NULL),
 
+
+  checkboxInput(inputId="capitalise",label="Correct capital letters (valid only for \"miR\" and \"let\")", value=FALSE)#,
+
+#  helpText("Substitute"),
+#  textInput("subst.orig",label=NULL,value=NULL),
+#  textInput("subst.fin",label=NULL,value="")
+
     ),    
 
     mainPanel(
       #textOutput("text2", container=span),
       helpText("Coincidences across miRNA versions"),
       plotOutput("percent"),
-
       textOutput("text1", container=span),
-
       helpText("Your translated miRNAs are:"),
-
       downloadButton("downloadTranslated",label="Download table"),
-
       tableOutput("translated")
-
-
-
     )
   )  
 ))