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Last data update: 2014.03.03

R: Scatter plots (dotplots) for flowPlates.

xyplot

R Documentation

Scatter plots (dotplots) for flowPlates.

Description

A function to create dotplots, and smoothed scatter plots, from flowPlates. This function is a slightly modified version of xyplot from flowViz. The flowPlate xyplot allows users to overlay plots of test samples versus controls, and makes creating informative flowStrips easier. Refer to the documentation for xyplot from flowViz and lattice for more detailed information.

Usage

## S4 method for signature 'formula,flowPlate'
xyplot(x, data, xlab, ylab,
				as.table = TRUE,
				prepanel = prepanel.xyplot.flowPlate,
				panel = panel.xyplot.flowPlate,
				pch = ".", smooth = TRUE,
				filter = NULL,
				filterResults = NULL,
				displayFilter = TRUE,
				flowStrip=NULL,
				flowStripCex=1,
				strip=function(...,style=1) strip.default(...,style=1),
				...)

Arguments

`x`	A formula describing the layout of the plots. Plots for flowPlates usually condition on either `as.factor(name)` or `as.factor(Well.Id)` since only one flowFrame can be shown on each panel (with the exception of Negative.Control overlays).
`data`	A flowPlate.
`xlab`	Label for x-axis.
`ylab`	Label for y-axis.
`as.table`	Defaults to table layout.
`prepanel`	Lattice-flowViz prepanel function.
`panel`	Lattice-flowViz panel function.
`pch`	Plotting character.
`smooth`	Plot a smoothed scatterplot by default.
`filter`	A flowCore filter to apply to each flowFrame.
`filterResults`	If filterResults="Negative.Control", the negative control wells corresponding to a test well are overlayed in the test well plots.
`displayFilter`	Defaults to displaying filter on the plot.
`flowStrip`	Character vector indicating additional information to be printed on the strip. Values can include any combination of "Well.Id","MFI","MFI.Ratio", and "Percent.Positive".
`flowStripCex`	Font size for the flowStrip.
`strip`	Lattice strip function.
`...`	Optional arguments

Author(s)

Errol Strain

Examples

library(plateCore)
data(plateCore)

# Create a flowPlate from the sample data in plateCore
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")

## Create a rectangle filter
rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))

xyplot(`SSC-H` ~ `FSC-H` | as.factor(name), 
	fp[1], smooth=FALSE, filter=rectGate, displayFilter=FALSE)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/xyplot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xyplot
> ### Title: Scatter plots (dotplots) for flowPlates.
> ### Aliases: xyplot xyplot-method xyplot,formula,flowPlate-method
> ### Keywords: methods dplot
> 
> ### ** Examples
> 
> library(plateCore)
> data(plateCore)
> 
> # Create a flowPlate from the sample data in plateCore
> fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")
> 
> ## Create a rectangle filter
> rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))
> 
> xyplot(`SSC-H` ~ `FSC-H` | as.factor(name), 
+ 	fp[1], smooth=FALSE, filter=rectGate, displayFilter=FALSE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>