cytoPlotDatabase3d: cytoPlotDatabase3d

Description Usage Arguments Value Examples

Description

A plot3d wrapper for a database (list) of cytometries as a mixture of multivariate normals as used in optimalFlowTemplates.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
cytoPlotDatabase3d(
  database.cytometries.as.mixtures,
  dimensions = c(1, 2, 3),
  xlim = c(0, 8000),
  ylim = c(0, 8000),
  zlim = c(0, 8000),
  xlab = "",
  ylab = "",
  zlab = "",
  colour = TRUE
)

Arguments

database.cytometries.as.mixtures

A list where each component is a mixture distribution. That is, each component is 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.

zlim

the z 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.

zlab

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

colour

If TRUE plots elements of a mixture distribution in different colours. If FALSE plots them in black.

Value

A three dimensional plot of ellipsoids containing the 95

Examples

1
2
3
4
5
6
7
8
9
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
  )
# # To execute requires an actual monitor since it uses rgl.
# cytoPlotDatabase3d(templates.optimalFlow$database.elliptical[which(templates.optimalFlow$clustering == 3)], dimensions = c(4,3), xlim = c(0, 8000), ylim = c(0, 8000), zlim = c(0, 8000), xlab = "", ylab = "", ylab = c(0, 8000))

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