added support of size and colour in ggplot2

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(pcaPlot)
+export(createES)
\ No newline at end of file

R/createES.R

+createES <- function(data, pData, labelDescription, colNames, rowNames) {
+  exprs <- data
+  colnames(exprs) <- colNames
+  truePData <- t(pData)
+  pd <- data.frame(truePData, row.names = colNames)
+  names(pd) <- labelDescription
+  require(Biobase)
+  phenoData <- AnnotatedDataFrame(pd)
+  featureData <- AnnotatedDataFrame(data.frame(rowNames))
+  es <- ExpressionSet(assayData = exprs, phenoData=phenoData, featureData = featureData)
+  return(es)
+}
\ No newline at end of file

R/pcaPlot.R

@@ -5,20 +5,39 @@
 #' @examples
 #' pcaPlot(es.norm, 1, 2) + aes(color=time)
 #' @export
-pcaPlot <- function(es, c1, c2) {
+pcaPlot <- function(es, columns, c1, c2, size="", colour="") {
   stopifnot(require(ggplot2))
-  pca <- prcomp(t(exprs(es)))
-
+  stopifnot(require(Biobase))
+  data <- t(exprs(es)[columns,])
+  pca <- prcomp(~., data.frame(data))
 
   explained <- (pca$sdev)^2 / sum(pca$sdev^2)
 
   xs <- sprintf("PC%s", seq_along(explained))
   xlabs <- sprintf("%s (%.1f%%)", xs, explained * 100)
 
-  pp <- ggplot(data=cbind(as.data.frame(pca$x), pData(es)))
+  pData <- pData(es)[!(rownames(pData(es)) %in% setdiff(rownames(pData(es)), rownames(pca$x))),]
+  pp <- ggplot(data=cbind(as.data.frame(pca$x), pData))
+  if (size == "" && colour == "") {
+    aes <- aes(x=eval(parse(text=xs[c1])),
+               y=eval(parse(text=xs[c2])))
+  } else if (size == "" && colour != "") {
+    c <- pData[[colour]];
+    aes <- aes(x=eval(parse(text=xs[c1])),
+               y=eval(parse(text=xs[c2])), colour=c)
+  } else if (size != "" && colour == "") {
+    s <- pData[[size]];
+    aes <- aes(x=eval(parse(text=xs[c1])),
+        y=eval(parse(text=xs[c2])), size=s)
+  } else {
+    s <- pData[[size]]
+    c <- pData[[colour]]
+    aes <- aes(x=eval(parse(text=xs[c1])),
+               y=eval(parse(text=xs[c2])), colour=c,size=s)
+  }
+  
   
   pp +
-    geom_point(aes(x=eval(parse(text=xs[c1])),
-                   y=eval(parse(text=xs[c2]))), size=3) +
+    geom_point(aes) +
     xlab(xlabs[c1]) + ylab(xlabs[c2])
 }

morpheusR.Rproj

@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes