boxplot.subset.proportion.stats: Stratified Boxplots of the Proportion of the Boolean/Existing...

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

Description

Creates a stratified boxplot of the per-patient proportions of the given subset. Iff booleanSubset is provided, adds the given booleanSubset to the gating tree first.

Usage

## S3 method for class 'subset.proportion.stats'
boxplot(gsOrGsListOrPath,
  existingSubset = NULL, booleanSubset = NULL, parentGate,
  parentGateForProportionCalc = parentGate, groupBy = NULL,
  outdir = NULL, overrideGate = FALSE, ylimits = NULL,
  baseSize = 19, sampleIDCol = NULL, jitterWidth = 0.15)

Arguments

gsOrGsListOrPath	Either a GatingSet, a GatingSetList, or path to one of these objects on disk
existingSubset	(existingSubset or booleanSubset must be provided) The name of the existing subset of interest, e.g. "CD3/GMM"
booleanSubset	(existingSubset or booleanSubset must be provided) The booleanSubset (a combination of existing gates) in string format, e.g. "8+/GMM+&!8+/GAMMADELTA"
parentGate	The gate under which the booleansubset is added
parentGateForProportionCalc	The parent gate which is to be used in proportion calculations (e.g. "8+" or "3+"). Defaults to parentGate
groupBy	optional string. What variable to stratify the boxplot by
outdir	Where to save the boxplot and stats, if desired.
overrideGate	If this is set to TRUE, booleanSubset will override any previous node of the same name under the same parentGate.
ylimits	optional numeric vector
sampleIDCol	(optional) Name of the GatingSet metadata column which contains individual sample identifiers. If sampleIDCol is provided, outliers will be labeled with this value.
jitterWidth

Value

boxplot and stats, and optionally saves the plot to outdir

Examples

## Not run: 
boxplot.subset.proportion.stats(gsOrGsListOrPath="/Path/To/GatingSet",
                                booleanSubset="GMM&GAMMADELTA",
                                parentGate="CD3",
                                groupBy="HIVStatus",
                                outdir="Path/To/Plot/Directory",
                                overrideGate=FALSE,
                                ylimits=NULL)

## End(Not run)

seshadrilab/flowHelpers documentation built on May 23, 2019, 4:05 a.m.