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Last data update: 2014.03.03

R: Plot flow cytometry data with density-based colors

plotDens

R Documentation

Plot flow cytometry data with density-based colors

Description

Generate a scatter dot plot with colors based on the distribution of the density of the provided channels.

Usage

plotDens(flow.frame, channels,  col, main, xlab, ylab, pch=".", s=FALSE, outdir, file.name, devn=TRUE, ...)

Arguments

`flow.frame`	a 'FlowFrame' object.
`channels`	a vector of two channel names or their corresponding indices in the 'flow.frame'.
`s`	logical variable, if TRUE the output graph is saved.
`outdir`	an optional string value specifying the output directory for saving the graph if 's' is TRUE.
`file.name`	an optional string value used as the name for the saved file.
`devn`	by default the output graph plots in a new device using dev.new() function. If 'devn' is FALSE, plots the output on the current device.
`col`	A specification for the default plotting color: see '?par'.
`main`	an overall title for the plot: see '?plot'
`xlab`	a title for the x axis: see '?plot'
`ylab`	a title for the y axis: see '?plot'
`pch`	Either an integer specifying a symbol or a single character to be used as the default in plotting points: see '?par'.
`...`	can be used to provide desired arguments for the plot() function used to plot the output results.

Value

a scatter dot plot with density-based colors.

Author(s)

Jafar Taghiyar <jtaghiyar@bccrc.ca> Mehrnoush Malek <mmalekes@bccrc.ca>

Examples


data_dir <- system.file("extdata", package = "flowDensity")
load(list.files(pattern = 'sampleFCS_1', data_dir, full = TRUE))
#Plot CD3 vs. CD19 to see the distribution of cell populations and their density
plotDens(f,c("V450-A","PerCP-Cy5-5-A"))

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(flowDensity)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowDensity/plotDens.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDens
> ### Title: Plot flow cytometry data with density-based colors
> ### Aliases: plotDens 'plot, flowFrame, CellPopulation-method'
> ### Keywords: Automated gating FlowCytData
> 
> ### ** Examples
> 
> 
> data_dir <- system.file("extdata", package = "flowDensity")
> load(list.files(pattern = 'sampleFCS_1', data_dir, full = TRUE))
> #Plot CD3 vs. CD19 to see the distribution of cell populations and their density
> plotDens(f,c("V450-A","PerCP-Cy5-5-A"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>