fix commit

R/pcaPlot.R

+#' Makes nice PCA plot for expression data
+#' @param es an ExpressionSet object, should be normalized
+#' @param c1 a number of the first component to plot (numeric)
+#' @param c2 a number of the second component to plot (numeric)
+#' @examples
+#' pcaPlot(es.norm, 1, 2) + aes(color=time)
+#' @export
+pcaPlot <- function(es, c1, c2) {
+  stopifnot(require(ggplot2))
+  pca <- prcomp(t(exprs(es)))
+
+
+  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)))
+
+  pp +
+    geom_point(aes(x=eval(parse(text=xs[c1])),
+                   y=eval(parse(text=xs[c2]))), size=3) +
+    xlab(xlabs[c1]) + ylab(xlabs[c2])
+}

man/pcaPlot.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pca_plot.R
+\name{pcaPlot}
+\alias{pcaPlot}
+\title{Makes nice PCA plot for expression data}
+\usage{
+pcaPlot(es, c1, c2)
+}
+\arguments{
+\item{es}{an ExpressionSet object, should be normalized}
+
+\item{c1}{a number of the first component to plot (numeric)}
+
+\item{c2}{a number of the second component to plot (numeric)}
+}
+\description{
+Makes nice PCA plot for expression data
+}
+\examples{
+pcaPlot(es.norm, 1, 2) + aes(color=time)
+}
+