some fixes

.gitignore

@@ -1 +1,2 @@
 .DS_Store
+.Rhistory

Rpackage/R/clustvis.R

@@ -54,7 +54,7 @@ createCaption = function(type, info){
     leg = append(leg, c("N = ", info$n[2], " data points."))
   } else if(type == "hm"){
     sc = convertIdsToNames(info$rowScaling)
-    scaling = str_c(sc, " is applied to ", changeRowsCols("rows", transp), ". ")
+    scaling = paste0(sc, " is applied to ", changeRowsCols("rows", transp), ". ")
     if(info$rowCentering){
       leg = append(leg, c(changeRowsCols("Rows", transp), " are centered; ", scaling))
     } else {
@@ -81,11 +81,11 @@ createCaption = function(type, info){
     }
     n = info$n
     if(transp) n = rev(n)
-    leg = append(leg, str_c(str_c(n, c(" rows", " columns.")), collapse = ", "))
+    leg = append(leg, paste(paste(n, c("rows", "columns.")), collapse = ", "))
   } else {
     stop("caption type is not supported!")
   }
-  stringr::str_c(leg, collapse = "")
+  paste(leg, collapse = "")
 }
 
 #read file and extract annotations
@@ -578,7 +578,7 @@ generatePCA = function(proc, pcx = 1, pcy = 2, switchDirX = FALSE, switchDirY =
     l = list(NULL, 0, 0, message = paste0("You have ", nColor, " different groups for color, only up to ", maxColorLevels, " are allowed. Please change color grouping!"))
     return(structure(l, class = "pca"))
   } else if(nShape > maxShapeLevels){
-    l = ist(NULL, 0, 0, message = paste0("You have ", nShape, " different groups for shape, only up to ", maxShapeLevels, " are allowed. Please change shape grouping!"))
+    l = list(NULL, 0, 0, message = paste0("You have ", nShape, " different groups for shape, only up to ", maxShapeLevels, " are allowed. Please change shape grouping!"))
     return(structure(l, class = "pca"))
   }
   ellCoord = calcEllipses(x2, ellipseConf)

Rpackage/vignettes/vignette.Rmd

@@ -24,8 +24,8 @@ This vignette shows some minimal examples how to generate plots using R package
 ```{r, fig.show = 'hold', fig.height = 4, fig.width = 7}
 library(clustvis)
 file = "https://raw.githubusercontent.com/taunometsalu/ClustVis/master/datasets/nki.csv"
-d = importData(file)
-proc = processData(d)
+imp = importData(file)
+proc = processData(imp)
 pca = generatePCA(proc)
 savePCA(pca, file = NA)
 ```
@@ -35,8 +35,8 @@ savePCA(pca, file = NA)
 ```{r}
 library(clustvis)
 file = "https://raw.githubusercontent.com/taunometsalu/ClustVis/master/datasets/nki.csv"
-d = importData(file)
-proc = processData(d)
+imp = importData(file)
+proc = processData(imp)
 hm = generateHeatmap(proc)
 saveHeatmap(hm, file = NA)
 ```

server.R

@@ -1136,8 +1136,8 @@ shinyServer(function(input, output, session) {
 
 	output$captionPCA = renderUI({
 	  data = getProc()
-	  info = getPCA()$captionInfo
     if(!is.null(data$matPca)){
+      info = getPCA()$captionInfo
       leg = createCaption(type = "pca", info = info)
       #http://stackoverflow.com/questions/23233497/outputting-multiple-lines-of-text-with-rendertext-in-r-shiny
       return(HTML("<h5>Caption example</h5><p>", leg, "</p>"))
@@ -1148,8 +1148,8 @@ shinyServer(function(input, output, session) {
 
 	output$captionHeatmap = renderUI({
 	  data = getProc()
-	  info = getHeatmap()$captionInfo
-    if(!is.null(info) && !is.null(data$matImputed) && all(dim(data$matImputed) <= maxDimensionHeatmap)){
+    if(!is.null(data$matImputed) && all(dim(data$matImputed) <= maxDimensionHeatmap)){
+      info = getHeatmap()$captionInfo
       leg = createCaption(type = "hm", info = info)
       return(HTML("<h5>Caption example</h5><p>", leg, "</p>"))
     } else {