plot.flowDens: Contour or Image Plot of Clustering Results

In RGLab/flowClust: Clustering for Flow Cytometry

Contour or Image Plot of Clustering Results

Description

This method makes use of the flowDens object returned by density to generate a contour or image plot.

Usage

## S4 method for signature 'flowDens,missing'
plot(
  x,
  type = c("contour", "image"),
  nlevels = 30,
  scale = c("raw", "log", "sqrt"),
  color = c("rainbow", "heat.colors", "terrain.colors", "topo.colors", "cm.colors",
    "gray"),
  xlab = colnames(x@dx),
  ylab = colnames(x@dy),
  ...
)

Arguments

x	The flowDens object returned from density.
type	Either "contour" or "image" to specify the type of plot desired.
nlevels	An integer to specify the number of contour levels or colors shown in the plot.
scale	If "log", the logarithm of the density values will be used to generate the plot; similar interpretation holds for "sqrt". The use of a log or sqrt elicits more information about low density regions.
color	A string containing the name of the function used to generate the desired list of colors.
xlab, ylab	Labels for the x- and y-axes respectively.
...	Other arguments to be passed to contour or image, for example, drawlabels and add. Once an image plot is generated, users may impose a contour plot on it by calling this function with an additional argument add=TRUE.

Author(s)

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

References

Lo, K., Brinkman, R. R. and Gottardo, R. (2008) Automated Gating of Flow Cytometry Data via Robust Model-based Clustering. Cytometry A 73, 321-332.

See Also

flowClust, density

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