plot.flowClust: Scatterplot of Clustering Results
In flowClust: Clustering for Flow Cytometry

Description Usage Arguments Note Author(s) References See Also

This method generates scatterplot revealing the cluster assignment, cluster boundaries according to the specified percentile as well as supplemental information like outliers or filtered observations.

plot(x, y, ...)

## S4 method for signature 'flowClust,missing'
plot(x, data, subset = c(1, 2),
  ellipse = T, show.outliers = T, show.rm = F, include = 1:(x@K),
  main = NULL, grayscale = F, col = (if (grayscale) gray(1/4) else
  2:(length(include) + 1)), pch = ".", cex = 0.6,
  col.outliers = gray(3/4), pch.outliers = ".", cex.outliers = cex,
  col.rm = 1, pch.rm = 1, cex.rm = 0.6, ecol = 1, elty = 1,
  level = NULL, u.cutoff = NULL, z.cutoff = NULL, npoints = 100,
  add = F, ...)

## S4 method for signature 'flowClustList,missing'
plot(x, data, subset = c(1, 2),
  ellipse = T, show.outliers = T, show.rm = F, include = 1:(x@K),
  main = NULL, grayscale = F, col = (if (grayscale) gray(1/4) else
  2:(length(include) + 1)), pch = ".", cex = 0.6,
  col.outliers = gray(3/4), pch.outliers = ".", cex.outliers = cex,
  col.rm = 1, pch.rm = 1, cex.rm = 0.6, ecol = 1, elty = 1,
  level = NULL, u.cutoff = NULL, z.cutoff = NULL, npoints = 501,
  add = F, ...)

`x`	Object returned from `flowClust`.
`y`	missing
`...`	Further graphical parameters passed to the generic function `plot`.
`data`	A matrix, data frame of observations, or object of class `flowFrame`. This is the object on which `flowClust` was performed.
`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`.
`ellipse`	A logical value indicating whether the cluster boundary is to be drawn or not. If `TRUE`, the boundary will be drawn according to the level specified by `level` or `cutoff`.
`show.outliers`	A logical value indicating whether outliers will be explicitly shown or not.
`show.rm`	A logical value indicating whether filtered observations will be shown or not.
`include`	A numeric vector specifying which clusters will be shown on the plot. By default, all clusters are included.
`main`	Title of the plot.
`grayscale`	A logical value specifying if a grayscale plot is desired. This argument takes effect only if the default values of relevant graphical arguments are taken.
`col`	Color(s) of the plotting characters. May specify a different color for each cluster.
`pch`	Plotting character(s) of the plotting characters. May specify a different character for each cluster.
`cex`	Size of the plotting characters. May specify a different size for each cluster.
`col.outliers`	Color of the plotting characters denoting outliers.
`pch.outliers`	Plotting character(s) used to denote outliers. May specify a different character for each cluster.
`cex.outliers`	Size of the plotting characters used to denote outliers. May specify a different size for each cluster.
`col.rm`	Color of the plotting characters denoting filtered observations.
`pch.rm`	Plotting character used to denote filtered observations.
`cex.rm`	Size of the plotting character used to denote filtered observations.
`ecol`	Color(s) of the lines representing the cluster boundaries. May specify a different color for each cluster.
`elty`	Line type(s) drawing the cluster boundaries. May specify a different line type for each cluster.
`level, u.cutoff, z.cutoff`	These three optional arguments specify the rule used to identify outliers. By default, all of them are left unspecified, meaning that the rule stated in `x@ruleOutliers` will be taken. Otherwise, these arguments will be passed to `ruleOutliers`.
`npoints`	The number of points used to draw each cluster boundary.
`add`	A logical value. If `TRUE`, add to the current plot.