plot_density_3D: Visualization of 3D Density of various groups on Principal...

In OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

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 <[e-mail]>

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)

OMICsPCA documentation built on Nov. 8, 2020, 5:01 p.m.