| showgate.FCS {rflowcyt} | R Documentation |
On an exisiting plot, the gate specified will be plotted and the datapoints lying within the gating range will be colored (default is the color purple).
showgate.FCS(data.mat, gatingrange, Index,
type = c("uniscut", "biscut", "bidcut", "bipcut"),
IndexValue.In = 1,
coltype = 12, pchtype = 8,
biscut.quadrant = c("+/-","-/-", "+/+", "-/+"))
data.mat |
the data to be gated:
|
gatingrange |
gating threshold range in one of the following
formats for each type of gating:
|
Index |
a vector of 0's and 1's denoting the selection of row observations of 'data.mat' |
type |
character string of the type of cut/gating:
|
IndexValue.In |
The value of 'Index' to be selected; default is 1 |
coltype |
a character string or a numerical value describing the option for the color of the data point inside the gating range |
pchtype |
a character string or a numerical value describing the option for the point size and type of data point inside the gating range |
biscut.quadrant |
character string value denoting the (x,y)
quadrant that is to be selected; Values are one of the following:
|
The gating range or gate will be displayed and the data points within the gating range will be colored.
The coloring in of data points may take a while to process. The gate
selection can only be shown using rectangular binning of the image
plots using ContourScatterPlot. The
showgate.FCS does not work with hexagonal binning.
A.J. Rossini and J.Y. Wan
FHCRC.HVTNFCS,VRC.HVTNFCS,
plotvar.FCS,createGate,
icreateGate
if (interactive()){
if (require(rfcdmin)){
## obtaining the FCS objects from VRC data
if ( !(is.element("unst.1829", objects())
& is.element("st.1829", objects())) ){
data(VRCmin)
}
## univariate plot
plotvar.FCS(unst.1829, type="uni", varpos=1, plotType=hist)
## show cut off at 350
showgate.FCS(unst.1829@data[,1], type="uniscut", gatingrange=350)
## show different cutoff at 500
showgate.FCS(unst.1829@data[,1], type="uniscut", gatingrange=500,
coltype="green")
## bivariate plot : rectanglar bins in which the gate can be shown
plotvar.FCS(unst.1829, type="bi", varpos=c(1,2), hexbin.CSPlot=FALSE)
## show cutoff at 275 to 600 for both variables
## may take a while
## create the gate index as the first column entry of the "gate" matrix
unst.1829.gt<-createGate(unst.1829, varpos=1:2, type="bidcut",
gatingrange=c(275, 600, 275, 600))
## show the gate
showgate.FCS(unst.1829.gt@data[,c(1,2)], unst.1829.gt@gate[,1],
type="bidcut", gatingrange=c(275, 600, 275, 600))
}
}