highlight.boolean.subset.flow.plot: Overlay and Highlight Polyfunctional Cell Subsets on a Flow...

In seshadrilab/COMPASSHelpers: Collection of helper functions for analyzing FCM data

Description

Defines a function to Overlay and Highlight Polyfunctional Cell Subsets on a Flow plot This function assumes there are two columns, conditioncol and conditioncol2, upon which you are stratifying the plots

Usage

highlight.boolean.subset.flow.plot(path, gsOrGsList = NULL,
  outdir = NULL, individualsCol, individual, conditioncol, exp, ctrl,
  conditioncol2 = ".", parentsubset, boolsubset, xaxis, yaxis,
  facetorder = NULL, facetorder2 = NULL, geomTextY = 5,
  geomTextX = 200, pngORsvg = "png", width = NULL,
  overlayDotSize = 0.4, themeBaseSize = 18,
  stripLegendGridAxesTitle = FALSE, xlims = NULL, ylims = NULL,
  axestitle_fontsize = NULL, font = NULL, percentage_fontsize = NULL,
  geom_hex_bins = 120)

Arguments

path	path to directory holding GatingSetList or GatingSet
gsOrGsList	GatingSet or GatingSetList object
outdir	(Optional) saves image in output directory, if given
individualsCol	column which defines individual
individual	value of individual(s) in individualsCol whose data you want to plot
conditioncol	name of the column that defines the main experimental condition, e.g. Antigen
exp	experimental value in conditioncol, e.g. ESAT-6
ctrl	control value in conditioncol, e.g. DMSO
conditioncol2	second condition on which to stratify Flow plots, e.g. "PATIENT ID"
parentsubset	unique name of parent node to use for plots
boolsubset	the full boolean subset to be used by booleanfilter()
xaxis	a marker name to plot on the x-axis
yaxis	a marker name to plot on the y-axis
facetorder	(Optional) the levels of conditioncol (e.g. Antigen) in the order you want displayed
facetorder2	(Optional) the levels of conditioncol2 (e.g. Time) in the order you want displayed
width	width, in inches, of the plot

Value

Flow plot, unless outdir is specified

Examples

## Not run: 
highlight.boolean.subset.flow.plot(path="/home/path/to/GatingSetListAllBatches",
                                   individualsCol="PTID",
                                   individual=12345678,
                                   conditioncol="Antigen",
                                   exp="ESAT-6",
                                   ctrl="DMSO",
                                   conditioncol2="Time",
                                   parentsubset="8+",
                                   boolsubset="8+/TNFa+&!8+/IFNg+&!8+/IL2+&!8+/IL4+",
                                   xaxis="TNFa",
                                   yaxis="IFNg",
                                   facetorder=c("DMSO", "ESAT-6"))
                                   
## End(Not run)

seshadrilab/COMPASSHelpers documentation built on May 6, 2019, 6:04 p.m.