cytoPlot: cytoPlot

Description Usage Arguments Value Examples

Description

A plot wrapper for cytometries as a mixture of multivariate normals as used in optimalFlowTemplates.

Usage

1
2
3
4
5
6
7
8
cytoPlot(
  cytometry.as.mixture,
  dimensions = c(1, 2),
  xlim = NULL,
  ylim = NULL,
  xlab = NULL,
  ylab = NULL
)

Arguments

cytometry.as.mixture

A list, where each element contains the parameters of a component of the mixture as a list with entries: mean, cov, weight and type.

dimensions

A vector containing the two variables on which to perform the projection.

xlim

the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed and leads to a ‘reversed axis’. The default value, NULL, indicates that the range of the finite values to be plotted should be used.

ylim

the y limits of the plot.

xlab

a label for the x axis, defaults to a description of x.

ylab

a label for the y axis, defaults to a description of y.

Value

A two dimensional plot of ellipses containing the 95

Examples

1
2
3
4
5
6
7
8
database <- buildDatabase(
  dataset_names = paste0('Cytometry', c(2:5, 7:9, 12:17, 19, 21)),
  population_ids = c('Monocytes', 'CD4+CD8-', 'Mature SIg Kappa', 'TCRgd-'))
templates.optimalFlow <-
  optimalFlowTemplates(
    database = database, templates.number = 5, cl.paral = 1
  )
cytoPlot(templates.optimalFlow$templates[[3]], dimensions = c(4, 3), xlim = c(0, 8000), ylim = c(0, 8000), xlab = "", ylab = "")

optimalFlow documentation built on Oct. 8, 2020, 2 a.m.