pcaPlot: PCA plot for harman results

In Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique

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.

Details

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

Value

None

See Also

harmanresults plot.harmanresults

Examples

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)

Harman documentation built on Nov. 8, 2020, 7:50 p.m.