density: Grid of Density Values for the Fitted t Mixture Model with...

In RGLab/flowClust: Clustering for Flow Cytometry

Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation

Description

This method constructs the flowDens object which is used to generate a contour or image plot.

Usage

## S4 method for signature 'flowClust'
density(
  x,
  data = NULL,
  subset = c(1, 2),
  include = 1:(x@K),
  npoints = c(100, 100),
  from = NULL,
  to = NULL
)

## S4 method for signature 'flowClustList'
density(
  x,
  data = NULL,
  subset = c(1, 2),
  include = 1:(x@K),
  npoints = c(100, 100),
  from = NULL,
  to = NULL
)

Arguments

x	Object returned from flowClust or from running filter on a flowFrame object.
data	A matrix, data frame of observations, or object of class flowFrame. This is the object on which flowClust or filter was performed. If this argument is not specified, the grid square upon which densities will be computed must be provided (through arguments from and to).
subset	A numeric vector of length two indicating which two variables are selected for the scatterplot. Alternatively, a character vector containing the names of the two variables is allowed if x@varNames is not NULL.
include	A numeric vector specifying which clusters are included to compute the density values. By default, all clusters are included.
npoints	A numeric vector of size two specifying the number of grid points in x (horizontal) and y (vertical) directions respectively.
from	A numeric vector of size two specifying the coordinates of the lower left point of the grid square. Note that, if this (and to) is not specified, data must be provided such that the range in the two variables (dimensions) selected will be used to define the grid square.
to	A numeric vector of size two specifying the co-ordinates of the upper right point of the grid square.

Details

The flowDens object returned is to be passed to the plot method for generating a contour or image plot.

Value

An object of class flowDens containing the following slots is constructed:

dx	A numeric vector of length npoints[1]; the x-coordinates of the grid points.
dy	A numeric vector of length npoints[2]; the y-coordinates of the grid points.
value	A matrix of size npoints[1] \times npoints[2]; the density values at the grid points.

Author(s)

Raphael Gottardo <[e-mail]>, Kenneth Lo <[e-mail]>

See Also

plot, flowClust

RGLab/flowClust documentation built on Jan. 31, 2024, 11:26 p.m.