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)) } }