plotPlate-methods: plotPlate

In plateCore: Statistical tools and data structures for plate-based flow cytometry

Description

Make a row vs. column plot of a plate, where the wells are colored according to some value of choice (number of events, median signal intensity, percent positive, etc.).)

Usage

plotPlate(fp, x = NA, method = "median", main, col, values, width = 1, na.action = "zero", ...)

Arguments

fp	A flowPlate.
x	A character indicating the variable of interest. Valid choices are "events", any single channel name (e.g. FSC-H, SSC-H, FL1-H, etc.), or vector of channel names if the method is mahalanobis.
method	Valid choices are mean, median, sd, mad, mahalanobis, or one of the numeric columns in the wellAnnotation data.frame (e.g. Percent.Positive, Positive.Count, MFI, MFI.Ratio)
main	Main text for the plot
col	Character vector of two colors.
values	Optional list of values, with names corresponding to sampleNames, that will be used for plotting.
width	Width of the well.
na.action	Handling of NA values, either "zero" or "omit".
...	optional arguments

Value

Plots the plate to the standard output.

Author(s)

Jon Gosink and Errol Strain

References

The original version of this plot came from the prada package.

Examples

library(plateCore)
data(plateCore)

## Create a flowPlate
fp <- flowPlate(pbmcPlate,wellAnnotation,"p1001")

plotPlate(transform("FL1-H"=log10) %on% fp,x="FL1-H",method="mean",col=c("yellow", "darkblue"))

plateCore documentation built on May 6, 2019, 2:41 a.m.