showgate.FCS {rflowcyt}R Documentation

Showing the gate and the datapoints within the gate on a prevous plot

Description

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).

Usage

showgate.FCS(data.mat, gatingrange, Index,
       type = c("uniscut", "biscut", "bidcut", "bipcut"),
       IndexValue.In = 1,
       coltype = 12, pchtype = 8,
       biscut.quadrant = c("+/-","-/-", "+/+", "-/+")) 

Arguments

data.mat the data to be gated:
univariate case
single column of values: a (m X 1) data vector where m is the number of cells/rows
bivariate case
matrix of two column variables: a (m X 2) data matrix where m is the number or cells/rows
gatingrange gating threshold range in one of the following formats for each type of gating:
"uniscut"
univariate single cut; gatingrange $=$ x1 will select/include all points $>=$ x1 , x1 is numeric value
"bidcut"
bivariate double cut: gatingrange $=$ c(x1,x2, y1,y2), a numeric vector of lowerbound, upperbound cutoffs for x and y variables
"biscut"
bivariate single cut:gatingrange$=$c(x1,y1), a numeric vector of the cutoffs for x and y variables
"bipcut"
bivariate polygonal cut: polygonal thresholds for an n-sided polygon with gatingrange $=$ cbind(c(x1, x2, ...,xn, x1), c(y1, y2, ...,yn, y1)), a vector of vectors which denote the outer points of the polygonal vertices)

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:
"uniscut"
univariate single cut: selects datapoints that are greater than or equal to the cutoff value denoted in gatingrange
"bidcut"
bivariate double cut: selects datapoints in the central rectangle formed by two vertical lines (x variable cutoffs) and two horizontal lines (y variable cutoffs)
"biscut"
bivariate single cut: cuts graph into quadrants (selects datapoints in the quadrant denoted by biscut.quadrant)
"bipcut"
bivariate polygonal cut: selects the datapoints in a polygon
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:
"$+$/$+$"
selects the upper right quadrant, where x is positive and y is positive
"$-$/$+$"
selects the upper left quadrant, where x is negative and y is positive
"$+$/$-$"
selects the lower right quadrant, where x is positive and y is negative
"$-$/$-$"
selects the lower left quadrant, where x is negative and y is negative

Value

The gating range or gate will be displayed and the data points within the gating range will be colored.

Note

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.

Author(s)

A.J. Rossini and J.Y. Wan

See Also

FHCRC.HVTNFCS,VRC.HVTNFCS, plotvar.FCS,createGate, icreateGate

Examples


  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))

    }
  }


[Package rflowcyt version 1.10.1 Index]