# plotPCA: A Function to Make a PCA Plot from an ExpressionSet or matrix In affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

## Description

This function makes a PCA plot from an ExpressionSet or matrix

## Usage

 ```1 2 3 4 5 6 7 8 9``` ```## S4 method for signature 'matrix' plotPCA(object, groups = NULL, groupnames = NULL, addtext = NULL, x.coord = NULL, y.coord = NULL, screeplot = FALSE, squarepca = FALSE, pch = NULL, col = NULL, pcs = c(1, 2), legend = TRUE, main = "Principal Components Plot", plot3d = FALSE, outside = FALSE, ...) ## S4 method for signature 'ExpressionSet' plotPCA(object, ...) ```

## Arguments

 `object` An `ExpressionSet` object or matrix. `groups` A numeric `vector` delineating group membership for samples. Default is `NULL`, in which case default plotting symbols and colors will be used. `groupnames` A character `vector` describing the different groups. Default is `NULL`, in which case the sample names will be used. `addtext` A character `vector` of additional text to be placed just above the plotting symbol for each sample. This is helpful if there are a lot of samples for identifying e.g., outliers. `x.coord` Pass an x-coordinate if automatic legend placement fails `y.coord` Pass a y-coordinate if automatic legend placement fails. `screeplot` Boolean: Plot a `screeplot` instead of a PCA plot? Defaults to `FALSE`. `squarepca` Should the y-axis of the PCA plot be made comparable to the x-axis? This may aid in interpretation of the PCA plot. Defaults to `FALSE`. `pch` A numeric `vector` indicating what plotting symbols to use. Default is `NULL`, in which case default plotting symbols will be used. Note that this argument will override the 'groups' argument. `col` A numeric or character `vector` indicating what color(s) to use for the plotting symbols. Default is `NULL` in which case default colors will be used. Note that this argument will override the 'groups' argument. `pcs` A character `vector` of length two (or three if plot3d is `TRUE`), indicating which principal components to plot. Defaults to the first two principal components. `legend` Boolean. Should a legend be added to the plot? Defaults to `TRUE`. `main` A character `vector` for the plot title. `plot3d` Boolean. If `TRUE`, then the PCA plot will be rendered in 3D using the rgl package. Defaults to `FALSE`. Note that the pcs argument should have a length of three in this case. `outside` Boolean. If `TRUE` the legend will be placed outside the plotting region, at the top right of the plot. `...` Further arguments to be passed to `plot`. See the help page for `plot` for further information.

## Value

This function returns nothing. It is called only for the side effect of producing a PCA plot or screeplot.

## Methods (by class)

• `ExpressionSet`:

## Author(s)

James W. MacDonald <[email protected]>

## Examples

 ```1 2 3 4 5``` ```library("affy") data(sample.ExpressionSet) plotPCA(sample.ExpressionSet, groups = as.numeric(pData(sample.ExpressionSet)[,2]), groupnames = levels(pData(sample.ExpressionSet)[,2])) ```

affycoretools documentation built on May 17, 2018, 6 p.m.