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.
Author(s)
James W. MacDonald <jmacdon@u.washington.edu>
Examples
library("affy")
data(sample.ExpressionSet)
plotPCA(sample.ExpressionSet, groups =
as.numeric(pData(sample.ExpressionSet)[,2]), groupnames =
levels(pData(sample.ExpressionSet)[,2]))
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(affycoretools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'affycoretools'
The following object is masked from 'package:BiocGenerics':
plotPCA
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affycoretools/plotPCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPCA
> ### Title: A Function to Make a PCA Plot from an ExpressionSet
> ### Aliases: plotPCA
> ### Keywords: hplot
>
> ### ** Examples
>
>
> library("affy")
> data(sample.ExpressionSet)
> plotPCA(sample.ExpressionSet, groups =
+ as.numeric(pData(sample.ExpressionSet)[,2]), groupnames =
+ levels(pData(sample.ExpressionSet)[,2]))
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.