pcaPlot: PCA plot for harman results

Description Usage Arguments Details Value See Also Examples

View source: R/pcaPlot.R

Description

Generates a Principle Component plot for an instance of harmanresults.

Usage

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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

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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)

JasonR055/Harman documentation built on May 7, 2019, 10:32 a.m.