cytoPlotDatabase3d {optimalFlow} | R Documentation |
A plot3d wrapper for a database (list) of cytometries as a mixture of multivariate normals as used in optimalFlowTemplates.
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 )
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. |
A three dimensional plot of ellipsoids containing the 95
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))