Description Usage Arguments Value Examples
View source: R/BoxplotBooleanSubsetcellProportions.R
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
1 2 3 |
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" |
Boxplot of the difference in cell proportions, unless outdir is given
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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)
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