Description Usage Arguments Examples
View source: R/LinePlotBooleanSubsetcellProportions.R
This function has a very specific purpose. It produces a paired line plot from a Time 1 to Time 2 of the background corrected proportions for a specified boolean subset. Patient replicates are collapsed and a T-test is performed across time. T-test and data are returned (if plot is saved to outdir) so that FDR can be applied later. http://www.annualreviews.org/doi/full/10.1146/annurev.publhealth.23.100901.140546#_i23
1 2 3 4 5 | lineplot.boolean.subset.proportions(path, gsOrGsList = NULL,
outdir = NULL, exp, ctrl, parentsubset, boolsubset, ylimits = NULL,
shortenTitle = FALSE, ctrlTrtCol, uniquePointCols, timeCol, time1Value,
time2Value, patientCol, titleHeader = NULL, gsSubset = NULL,
labelPoints = FALSE, showPvalue = TRUE, pngORsvg = "png")
|
path |
path to directory holding GatingSetList or GatingSet |
exp |
Value of ctrlTrtCol identifying stimulated samples |
ctrl |
Value of ctrlTrtCol identifying unstimulated samples |
ctrlTrtCol |
Name of the column of metadata which identified whether a sample is treatment or control. The column should contain 2 values. |
uniquePointCols |
Name(s) of column(s) of metadata which identify a set of samples as being measurements from one patient's specific time point. |
timeCol |
Name of column which identifies timepoints 1 and 2 |
time1Value |
timepoint 1 value |
time2Value |
timepoint 2 value |
patientCol |
Name of column which identifies a unique patient/individual across all times and treatments |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
lineplot.boolean.subset.proportions(path=gatingSetListDir,
outdir="/home/out/PostCompassPlots",
ctrlTrtCol="Treatment",
exp="UV HSV-2",
ctrl="Mock",
timeCol="Day",
parentsubset="CD4+ CD8-",
boolsubset="!CD40L+&!IFNg+&!IL2+&TNFa+",
ylimits=NULL,
shortenTitle=TRUE,
titleHeader="",
uniquePointCols="$SRC",
gsSubset=gsGroup1Indices,
patientCol="Patient")
## End(Not run)
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