lineplot.boolean.subset.proportions: lineplot.boolean.subset.proportions

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

Description

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

Usage

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")

Arguments

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

Examples

## 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)

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