runTSNE: run tSNE from (R pkg 'Rtsne') on a gatingSet Will sample the...

In RGLab/flowIncubator: Routines that don't belong to the core flow packages yet.

Description

IMPORTANT: Requires a valid gatingSet with cytokine gates downstream of a parent gate Also expects that pData(gs) contains at least columns: 'name', 'ptid' so we can identify cells later

Usage

runTSNE(gs, parentGate, cytokines, otherMarkers, markerMap, swap = FALSE,
  groupBy, degreeFilter = 0, seed = 999, theta = 0.9, ...)

Arguments

gs	a GatingSet object, properly gated data with annotation in its pData
parentGate	a string describing the gate upstream of the cytokine gates (eg. "CD4", "cd8+", etc...)
otherMarkers	the remaining markers of the data
markerMap	named list of marker names to gate names, eg. list("CD4/IL2" = "IL2","CD4/IFNg" = "IFNg")
swap	boolean for whether marker and gate names (from markerMap above) should be swapped. Passed onto getSingleCellExpression()
groupBy	columns of the gatingSet's phenoData, same number of cells will be sampled from each group
degreeFilter	keep cells of this degree and higher, useful when tSNE takes too long to run
seed	since tSNE is random, need a random seed so we can reproduce results
theta	parameter to be passed to the Rtsne function
...	other parameters to be passed to the Rtsne function
cytokine	a vector of strings describing the cytokine gates immediately downstream of parentGate, eg: "IL2", "IFNg"

Value

a matrix of X and Y coordinates

RGLab/flowIncubator documentation built on Sept. 5, 2020, 11:10 p.m.