From 37f094272fc3d8147ebca16fc0db72e390cbad55 Mon Sep 17 00:00:00 2001
From: Daria Zenkova <darya.nightmare@gmail.com>
Date: Thu, 1 Sep 2016 16:07:33 +0300
Subject: [PATCH] added support of size and colour in ggplot2

---
 NAMESPACE       |  1 +
 R/createES.R    | 12 ++++++++++++
 R/pcaPlot.R     | 33 ++++++++++++++++++++++++++-------
 morpheusR.Rproj |  5 +++++
 4 files changed, 44 insertions(+), 7 deletions(-)
 create mode 100644 R/createES.R

diff --git a/NAMESPACE b/NAMESPACE
index 5b9879b..328b0b5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
 export(pcaPlot)
+export(createES)
\ No newline at end of file
diff --git a/R/createES.R b/R/createES.R
new file mode 100644
index 0000000..1a323f8
--- /dev/null
+++ b/R/createES.R
@@ -0,0 +1,12 @@
+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
diff --git a/R/pcaPlot.R b/R/pcaPlot.R
index 7a33e62..13802f7 100644
--- a/R/pcaPlot.R
+++ b/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])
 }
diff --git a/morpheusR.Rproj b/morpheusR.Rproj
index d848a9f..cba1b6b 100644
--- a/morpheusR.Rproj
+++ b/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
 
-- 
GitLab