there are labels in morpheus.js now

R/createES.R

 createES <- function(data, pData, labelDescription, colNames, rowNames) {
-  exprs <- data
+  exprs <- t(data)
   colnames(exprs) <- colNames
   truePData <- pData
   pd <- data.frame(truePData, row.names = colNames)

R/pcaPlot.R

@@ -5,11 +5,13 @@
 #' @examples
 #' pcaPlot(es.norm, 1, 2) + aes(color=time)
 #' @export
-pcaPlot <- function(es, columns=c(), rows=c(), c1, c2, size="", colour="") {
+pcaPlot <- function(es, columns=c(), rows=c(), c1, c2, size="", colour="", label="") {
   n1 <- as.numeric(c1)
   n2 <- as.numeric(c2)
   stopifnot(require(ggplot2))
+  stopifnot(require(ggrepel))
   stopifnot(require(Biobase))
+  stopifnot(require(svglite))
   
   if (is.null(rows)) {
     rows <- 1:nrow(exprs(es))
@@ -24,17 +26,17 @@ pcaPlot <- function(es, columns=c(), rows=c(), c1, c2, size="", colour="") {
   data <- t(exprs(es)[rows,columns])
   pca <- prcomp(data)
   explained <- (pca$sdev)^2 / sum(pca$sdev^2)
-
+  
   xs <- sprintf("PC%s", seq_along(explained))
   xlabs <- sprintf("%s (%.1f%%)", xs, explained * 100)
-
+  
   pData <- pData(es)[!(rownames(pData(es)) %in% setdiff(rownames(pData(es)), rownames(pca$x))),]
   
   if (size != "") {
     pData[[size]] <- as.numeric(pData[[size]])
   }
   
-  pp <- ggplot(data=cbind(as.data.frame(pca$x), pData))
+  pp <- ggplot(data=cbind(as.data.frame(pca$x), pData, sampleNames(es)))
   if (size != "" && colour != "") {
     
     aes <- aes_string(x=xs[n1],
@@ -42,16 +44,32 @@ pcaPlot <- function(es, columns=c(), rows=c(), c1, c2, size="", colour="") {
     
   } else if (colour != "") {
     aes <- aes_string(x=xs[n1],
-               y=xs[n2], colour=colour)
+                      y=xs[n2], colour=colour)
   } else if (size != "") {
     aes <- aes_string(x=xs[n1],
-        y=xs[n2], size=size)
+                      y=xs[n2], size=size)
   } else {
     aes <- aes_string(x=xs[n1],
                       y=xs[n2])
   }
   
-  pp +
-    geom_point(aes) +
+  g <- pp + aes + 
+    geom_point() + 
     xlab(xlabs[n1]) + ylab(xlabs[n2])
+  
+  if (label == "id") {
+    label <- "sampleNames(es)"
+  }
+  if (label != "") {    
+    message("i'm here 2s")
+    g <- g + geom_text_repel(aes_string(label=label))
+    
+  }
+  f <- tempfile(pattern="plot",tmpdir="~/morpheus.js/tmp",fileext=".svg")
+  ggsave(f, g)
+  
+  
+  
+  print(capture.output(str(g)))
+  return(f)
 }