An object returned by the function pca of the R package
pcaMethods.
plot.dim
A vector of 2 positive-integer-value integer specifying
which 2 pcas will be plot.
labelVariable
The name of a column of the phenotype data matrix. The elements
of the column will replace the column names of the expression data matrix.
hybName
character string. indicating the phenotype variable Hybridization_Name.
outFileName
Name of the figure file to be created.
title
Title of the scatter plot.
plotOutPutFlag
logical. plotOutPutFlag=TRUE indicates the plots will be output
to pdf format files. Otherwise, the plots will not be output
to external files.
mar
A numerical vector of the form 'c(bottom, left, top, right)'
which gives the number of lines of margin to be specified on
the four sides of the plot. The default is 'c(5, 4, 4, 2) +
0.1'. see par.
lwd
The line width, a _positive_ number, defaulting to '1'.
see par.
equalRange
logical. Indicating if the x-axis and y-axis have the same range.
xlab
Label of x axis.
ylab
Label of y axis.
xlim
Range of x axis.
ylim
Range of y axis.
cex.legend
Font size for legend.
cex
numerical value giving the amount by which plotting text
and symbols should be magnified relative to the default.
see par.
cex.lab
The magnification to be used for x and y labels relative to the current
setting of cex.
cex.axis
The magnification to be used for axis annotation relative to the current
setting of cex.
see par.
legendPosition
Position of legend.
Possible values are “bottomright”, “bottom”,
“bottomleft”, “left”, “topleft”,
“top”, “topright”, “right” and “center”.
...
Arguments to be passed to plot.
Value
A matrix of PCA scores. Each column corresponds to a principal component.
Author(s)
Weiliang Qiu <stwxq@channing.harvard.edu>,
Brandon Guo <brandowonder@gmail.com>,
Christopher Anderson <christopheranderson84@gmail.com>,
Barbara Klanderman <BKLANDERMAN@partners.org>,
Vincent Carey <stvjc@channing.harvard.edu>,
Benjamin Raby <rebar@channing.harvard.edu>