Description Usage Arguments Value Examples
View source: R/BoxplotSubsetProportionStats.R
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.
1 2 3 4 5 6 |
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 |
boxplot and stats, and optionally saves the plot to outdir
1 2 3 4 5 6 7 8 9 10 | ## 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)
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