plotDens: Plot flow cytometry data with density-based colors

In mehrnoushmalek/flowDensity: Sequential Flow Cytometry Data Gating

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

Arguments

obj	a 'FlowFrame', or 'cellPopulation' object.
channels	a vector of two channel names or their corresponding indices in the 'flow.frame'.
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'
pch	Either an integer specifying a symbol or a single character to be used as the default in plotting points: see '?par'.
density.overlay	Logical vector of length 2, to plot density overlays on the x and y axes. Default is c(FALSE,FALSE).
count.lim	Cutoff for number of events to set color. Default is 20. Samples with less than 20 cells will be plotted in black.
dens.col	2-character string giving the color of plot desired for density curves.
cex	Size of the points for the plot. For more information look at ?plot in graphics.
dens.type	2-character string giving the type of plot desired.
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.
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
show.contour	Default is FALSE. It add the contourLines to plot.
contour.col	Color for contourLines. Default is darkgrey.
verbose	Default is True. It will add that the sample has 0 cells in the plot title.
...	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 <[e-mail]> Jafar Taghiyar <[e-mail]>

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"))

mehrnoushmalek/flowDensity documentation built on Oct. 31, 2023, 1:27 a.m.