pplot: Draw a FlowJo-style (sort of) Plot

In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions

Draw a FlowJo-style (sort of) Plot

Description

Draw a picture, with colors reminiscent of FlowJo. NOTE: this function is deprecated. Please consider using ggflow instead.

Usage

pplot(
  ff,
  parameters,
  blueBackground = FALSE,
  showZero = FALSE,
  nbin = 501,
  bandwidth = 0.001,
  cr = blob_color(blueBackground = FALSE),
  col = "black",
  nrpoints = 0,
  max_channel = 262143,
  tx = c("biexp", "asinh", "log", "linear"),
  ty = c("biexp", "asinh", "log", "linear"),
  plotaxt = TRUE,
  ticksize = 1,
  ...
)

Arguments

ff	The flowFrame to be plotted
parameters	A vector of two parameters in ff. May be either character or numeric
blueBackground	Logical, should the background be blue. If false, you'll get a white background (like FlowJo)
showZero	Logical, draw dot-dash lines indicating the location of zero on each axis
nbin	Binning resolution (you shouldn't have to mess with the default)
bandwidth	Binning bandwidth (you shouldn't have to mess with the default)
cr	Color ramp. The only one supplied currently is the default
col	Not sure about this one, but the default is ok
nrpoints	Not sure about this one, but the default is ok
max_channel	Max value the cytometer can produce. See ax
tx	tick style. One of 'biexp', 'log', 'linear'
ty	tick style. One of 'biexp', 'log', 'linear'
plotaxt	Logical, should we draw the axes?
ticksize	Weight of the tickmarks in relative coordinates.
...	Additional graphical parameters passed to flowCore flowFrame-class

Examples

# get some example data
filename = system.file("extdata", "example1.fcs", package = "wadeTools")
ff = get_sample(filename)

# a plot with linear coordinate scaling
pplot(ff, parameters = c("FSC-A", "SSC-A"), tx = 'linear', ty = 'linear')

# another plot, with the default biexponential scaling
pplot(ff, c("CD4PETR", "CD8Q705"))

rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.