plot_density_3D {OMICsPCA} | R Documentation

## Visualization of 3D Density of various groups on Principal components

### Description

This function displays density of individuals from various groups created by create_group(). This wraps "persp" from package "graphics" and thus takes additional graphical input shown in example.

### Usage

    plot_density_3D(name, Assay, group, PC1 = 1,
    PC2 = 2, static = FALSE,
    gridsize = 100, groupinfo = NULL, ...)

### Arguments

`name` | Name of the "PCA" object containing the assay data
`Assay` | Name of an Assay
`group` | Names of a group
`PC1, PC2` | Numbers corresponding to the principal components on which density is to be calculated
`static` | Logical if TRUE a static plot is generated. default = FALSE
`gridsize` | A number used in kernel smoothing. default is 100
`groupinfo` | Same as integrate_variables()
`...` | additional arguments passed to base function "persp" from package "graphics"

### Details

2D density is calculated using the "kde2d"" function from package "MASS"" which use kernel density estimation (KDE) to calculate density of 2D data. If the variance on either or both of the PCs are 0, the KDE can't be calculated.

### Value

Displays 3D density plots of PCs

### Author(s)

Subhadeep Das <subhadeep1024@gmail.com>

### Examples

    PCAlist <- integrate_variables(Assays = c("H2az"),
    name = multi_assay,
    groups = c("WE","RE"), groupinfo = groupinfo_ext,
    scale.unit = FALSE, graph = FALSE)

    plot_density_3D(name = PCAlist, Assay = "H2az",
    group = "WE", PC1 = 1, PC2 = 2, grid_size = 100,
    static = FALSE, groupinfo = groupinfo_ext)

[Package OMICsPCA version 1.10.0 Index]