rectangleGate-class {flowCore} | R Documentation |
A convenience method to facilitate the construction of filter
objects
rectangleGate( filterId = "rectangleGate", .gate, ...) polygonGate(filterId = "polygonGate", boundaries, ...) polytopeGate(filterId = "polytopeGate", .gate, ...)
filterId |
An optional parameter that sets the filterId of this gate. |
.gate |
A definition of the gate. This can be either a list or matrix, described below. |
boundaries |
A definition of the gate. |
... |
You can also directly describe a gate without wrapping it in a list, as described below. |
This function is designed to be useful in both direct and programmatic usage.
For rectangle gate in n dimensions, if n=1 the gate correspond to a
range gate. If n=2, the gate is a rectangle gate. To use this function
programmatically, you may either construct a list
or you may construct a matrix with n
columns and 2
rows. The first row corresponds to the minimal value for each parameter
while the second row corresponds to the maximal value for each
parameter. The names of the parameters are taken from the
column names as in the third example.
For polygone gate, the boundaries are specified as vertices in 2 dimensions.
Returns a rectangleGate
or
polygonGate
object for use in filtering flowFrame
s or
other flow cytometry objects.
B. Ellis N. Le Meur
data(GvHD) #Create directly. Most likely from a command line rectangleGate(filterId="rectangleGateI","FSC-H"=c(1,50),"SSC-H"=c(50,800)) #To facilitate programmatic construction we also have the following rectangleGate(filterId="rectangleGateII",list("FSC-H"=c(1,50),"SSC-H"=c(50,800))) m <- matrix(c(1,50,50,800),ncol=2) colnames(m) <- c("FSC-H","SSC-H") rect <- rectangleGate(filterId="rectangleGate", m) pop1 <- filter(GvHD,rect) sub <- Subset(GvHD, pop1) ## PolygonGate sqrcut <- matrix(c(300,300,600,600,50,300,300,50),ncol=2,nrow=4) colnames(sqrcut) <- c("FSC-H","SSC-H") polygonGate(filterId="nonDebris", boundaries= sqrcut)