pcaPlot: PCA plot for harman results

Description

Generates a Principle Component plot for an instance of harmanresults.

Usage

pcaPlot(harmanresults, pc_x = 1, pc_y = 2, this = "corrected", colBy = "batch", pchBy = "expt", palette = "rainbow", legend = TRUE, col, pch, ...)

Arguments

harmanresults

An instance of harmanresults.

pc_x

integer, principle component for the plot x dimension.

pc_y

integer, principle component for the plot y dimension.

this

string, legal values are original or corrected.

colBy

string, colour the points by the experimental or batch variable; legal values are expt and batch. The palette function specified in palette is used. This parameter is overridden by col.

pchBy

string, point-type by the experimental or batch variable; legal values are expt and batch. This parameter is overridden by pch.

palette

string, the function to call to create a vector of contiguous colours with the levels of factor in colBy steps.

legend

logical, whether to display a legend on the plot.

col,

colour vector for the points. This parameter overrides colBy and palette.

pch,

integer vector giving the point type. This parameter overrides pchBy.

...

further arguments passed to or from other methods.

Value

None

Details

If a vector of colours is supplied via the col argument, then a legend will not be drawn.

Examples

Run this code

library(HarmanData)
data(OLF)
expt <- olf.info$Treatment
batch <- olf.info$Batch
olf.harman <- harman(as.matrix(olf.data), expt, batch)
pcaPlot(olf.harman)
pcaPlot(olf.harman, colBy='expt')
pcaPlot(olf.harman, pc_x=2, pc_y=3, this='original', pch=17)