cytoPlot3d: cytoPlot3d

Description Usage Arguments Value Examples

Description

A rgl::plot3d wrapper for cytometries as a mixture of multivariate normals as used in optimalFlowTemplates.

Usage

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cytoPlot3d(
  cytometry.as.mixture,
  dimensions = c(1, 2),
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = 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 three 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.

Value

A three dimensional plot of ellipsoids containing the 95

Examples

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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.
# cytoPlot3d(templates.optimalFlow$templates[[3]], dimensions = c(4, 3, 9), xlim = c(0, 8000), ylim = c(0, 8000), zlim = c(0, 8000), xlab = "", ylab = "", zlab = ")

HristoInouzhe/optimalFlow documentation built on April 24, 2020, 4:31 a.m.