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Last data update: 2014.03.03

R: plotPlate

plotPlate

R Documentation

plotPlate

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"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(plateCore)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

The following object is masked from 'package:flowViz':

    ecdfplot

sROC 0.1-2 loaded
No methods found in "flowStats" for requests: %on%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/plateCore/plotPlate-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPlate
> ### Title: plotPlate
> ### Aliases: plotPlate plotPlate-method plotPlate,flowPlate-method
> ### Keywords: methods
> 
> ### ** 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"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>