Description Usage Arguments Value Examples
View source: R/HighlightBooleanSubsetFlowPlot.R
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
1 2 3 4 5 6 7 8 9 | 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)
|
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 |
Flow plot, unless outdir is specified
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## 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)
|
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