From 71b2e93e6bba813c4d5988cf132bef1894fdf7ea Mon Sep 17 00:00:00 2001
From: Daria Zenkova <darya.nightmare@gmail.com>
Date: Wed, 17 Aug 2016 15:38:16 +0300
Subject: [PATCH] fix commit

---
 R/pcaPlot.R    | 24 ++++++++++++++++++++++++
 man/pcaPlot.Rd | 22 ++++++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 R/pcaPlot.R
 create mode 100644 man/pcaPlot.Rd

diff --git a/R/pcaPlot.R b/R/pcaPlot.R
new file mode 100644
index 0000000..7a33e62
--- /dev/null
+++ b/R/pcaPlot.R
@@ -0,0 +1,24 @@
+#' 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])
+}
diff --git a/man/pcaPlot.Rd b/man/pcaPlot.Rd
new file mode 100644
index 0000000..7abd70a
--- /dev/null
+++ b/man/pcaPlot.Rd
@@ -0,0 +1,22 @@
+% 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)
+}
+
-- 
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