plotDens: Plot flow cytometry data with density-based colors

Description Usage Arguments Value Author(s) Examples

View source: R/flowDensity_methods.R

Description

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

Usage

1
2
plotDens(obj, channels,node=NA ,col, main, xlab, ylab, xlim,ylim, pch=".", density.overlay=c(FALSE,FALSE),count.lim=20, dens.col=c("grey48","grey48"),cex=1,verbose=TRUE,
dens.type=c("l","l"),transparency=1, adjust.dens=1,show.contour=F, contour.col="darkgrey", ...)

Arguments

obj

a 'FlowFrame','GatingHierarchy' or 'cellPopulation' object.

channels

a vector of two channel names or their corresponding indices in the 'flow.frame'.

node

Only used if gatingHierarchy is provided as an input.It subtractes the flowFrame from the node of gatingHierarchy. see getNodes() in flowWorkspace.

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'

xlim

a range for the x axis: see '?plot'

ylim

a range for the y axis: see '?plot'

density.overlay

Logical vector of length 2, to plot density overlays on the x and y axes. Default is c(FALSE,FALSE).

density.type

2-character string giving the type of plot desired, see type in '?plot'

density.col

2-character string giving the color of plot desired for density curves.

transparency

Transparency of the bi-variate plot, to see the densitu curves in the background. The lower it is, the more transparent the plot is.

show.contour

Default is FALSE. It add the contourLines to plot.

contour.col

Color for contourLines. Default is darkgrey.

adjust.dens

The smoothness of density in [0,Inf] to be used in density(.). The default value is 1 and should not be changed unless necessary

count.lim

Cutoff for number of events to set color. Default is 20. Samples with less than 20 cells will be plotted in black.

verbose

Default is True. It will add that the sample has 0 cells in the plot title.

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, along with density overlays if desired. Set xlim and ylim when plotting if you would like to have all your plots to have same range on the axes (specially when density.overlay=TRUE)

Author(s)

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

Examples

1
2
3
4
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"))

mehrnoushmalek/flowDensity documentation built on July 28, 2021, 12:10 p.m.