cytoPlotDatabase: cytoPlotDatabase

In HristoInouzhe/optimalFlow: optimalFlow

cytoPlotDatabase

Description

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

Usage

cytoPlotDatabase(
  database.cytometries.as.mixtures,
  dimensions = c(1, 2),
  xlim = c(0, 8000),
  ylim = c(0, 8000),
  xlab = "",
  ylab = "",
  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.
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.
colour	If TRUE plots elements of a mixture distribution in different colours. If FALSE plots them in black.

Value

A two dimensional plot of ellipses containing the 95

Examples

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
  )
cytoPlotDatabase(templates.optimalFlow$database.elliptical[which(templates.optimalFlow$clustering == 3)], dimensions = c(4,3), xlim = c(0, 8000), ylim = c(0, 8000), xlab = "", ylab = "")

HristoInouzhe/optimalFlow documentation built on April 23, 2023, 5:45 p.m.