arrowPlot: PCA before and after arrow plot for harman results

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

Description

Generates an arrow plot for an instance of harmanresults. The tail of the arrow is the starting point (original) in principle coordinates, while the arrow head is the new point (corrected) in principle coordinates. It can be observed that on principle components that have undergone correction (codeharmanresults$stats$correction < 1.0), the samples within a batch will be coordinately moved towards 0 on that priciple component.

Usage

arrowPlot(harmanresults, pc_x = 1, pc_y = 2, colBy = "batch",
  palette = "rainbow", col, length = 0.1, legend = TRUE, ...)

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.
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.
palette	string, the function to call to create a vector of contiguous colours with the levels of factor in colBy steps.
col,	colour vector for the points. This parameter overrides palette.
length	length of the arrow heads, default is 0.1.
legend	logical, whether to display a legend on the plot
...	further arguments passed to or from other methods.

Details

Generates a Principle Component plot for an instance of harmanresults. 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(olf.data, expt, batch)
arrowPlot(olf.harman, pc_x=2, pc_y=3, length=0.2)

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