boxplot.boolean.subset.proportions: Boxplot of the difference in cell proportions for a given...

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

Description

This function creates a boxplot of the difference in cell proportions for a given condition (e.g. Antigen) across another variable (e.g. Time) for the specified boolean subset

Usage

boxplot(path, outdir = NULL,
       conditioncol, exp, ctrl, conditioncol2 = ".", parentsubset, boolsubset,
       ylimits = NULL, shortenTitle = FALSE, uniqueSamplesCol)

Arguments

outdir	(Optional), saves image in output directory if given
ylimits	(Optional), yaxis limits. numeric vector
shortenTitle	(Optional), a Boolean which specifies whether to shorten the title (overriden by titleHeader)
titleHeader	(Optional), a string containing the title of the plot (overrides the default)
gsSubset	(Optional), for now, just a numeric vector containing indices by which to subset gs for the plot. In the future, perhaps a logical expression on "gs" to limit the GatingSet(List) data used, e.g. which(pData(gs)$PatientTreatment == 'HSV529')
path:	path to directory holding GatingSetList
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:	condition on which to stratify box plots
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
uniqueSamplesCol:	pData column which defines unique samples, e.g. "Time.PTID"

Value

Boxplot of the difference in cell proportions, unless outdir is given

Examples

## Not run: 
boxplot.boolean.subset.proportions(path="/home/GatingSetListAllBatches",
                                   conditioncol="Antigen",
                                   exp="ESAT-6",
                                   ctrl="DMSO",
                                   conditioncol2="Time",
                                   parentsubset="8+",
                                   boolsubset="8+/TNFa+&!8+/IFNg+&!8+/IL2+&!8+/IL4+",
                                   ylimits=c(0, 0.013),
                                   uniqueSamplesCol="Time.PTID")
                                   
## End(Not run)

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