PlotPC2D: MetaPCA: Meta-analysis in the Dimension Reduction of Genomic...

In MetaPCA: MetaPCA: Meta-analysis in the Dimension Reduction of Genomic data

Description

2D PCA plots.

Usage

PlotPC2D(coord, drawObjects=TRUE, drawEllipse=FALSE, dataset.name=NULL, 
		pctInfo=NULL, main=NULL, sub=NULL, xlab=NULL, ylab=NULL, newPlot=TRUE, 
		.points.size=1, .class=rownames(coord), .class.order=NULL, .class.color=NULL, 
		.class2=NULL, .class2.order=NULL, .class2.shape=NULL, .annotation=TRUE, 
		.legend=c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"))

Arguments

coord	2D Coordinates matrix of objects. Rows are objects and columns are coordinates.
drawObjects	Whether to draw objects as points.
drawEllipse	Whether to draw ellipses estimated from objects 2D distribution.
dataset.name	Name to be displayed as a part of title.
pctInfo	Explained percentage of variance by each PC.
main	Main title.
sub	Sub title.
xlab	Label for x-axis.
ylab	Label for y-axis.
newPlot	Whether to draw a plot in the new frame.
.points.size	Size of objects' points.
.class	Object's class label such as disease classification.
.class.order	The order of class representation.
.class.color	The color of class representation.
.class2	The second class label of each object such as study name.
.class2.order	The order of 2nd class representation.
.class2.shape	The shape of 2nd class representation.
.annotation	Whether to present annotation such as x,y axis labels, legend, or titles.
.legend	Location of legend in a plot.

Value

NA. A PCA plot is drawn.

Author(s)

Don Kang ([e-mail]) and George Tseng ([e-mail])

References

Dongwan D. Kang and George C. Tseng. (2011) Meta-PCA: Meta-analysis in the Dimension Reduction of Genomic data.

Examples

## Not run: 
	#4 prostate cancer data which have three classes: normal, primary, metastasis
	data(prostate)
	metaPC <- MetaPCA(prostate, method="Angle", doPreprocess=FALSE)
	#Plotting 4 data in the same space with ellipses overlayed!
	coord <- foreach(dd=iter(metaPC$x), .combine=rbind) %do% dd$coord
	PlotPC2D(coord[,1:2], drawEllipse=T, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"), 
			.class.color=c('red','#838383','blue'), .annotation=T, newPlot=T,
			.class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))), 
			.class2.order=names(metaPC$x), .points.size=1)


## End(Not run)

MetaPCA documentation built on May 2, 2019, 11:03 a.m.