plotPlate-methods: plotPlate

Description Usage Arguments Value Author(s) References Examples

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

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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

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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 2, 2018, 4:36 a.m.