plot_integrated_density_3D: Visualization of 3D Density of various groups on Principal...

Description Usage Arguments Details Value Author(s) Examples

View source: R/plot_density_3D.R

Description

works similarly as "plot_density_3D" . See vignettes and man page of "plot_density_3D" for more details.

Usage

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plot_integrated_density_3D(name, PC1 = 1, PC2 = 2, group,
gridsize = 100, static = FALSE, groupinfo = NULL, ...)

Arguments

name

Name of the integrated "PCA" object

PC1, PC2

Numbers corresponding to the principal components on which density is to be calculated

group

Names of a group

gridsize

A number used in kernel smoothing. default is 100

static

Logical if TRUE a static plot is generated. default = FALSE

groupinfo

same as integrate_variables()

...

additional arguments allowed to base function "persp" of 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.

Author(s)

Subhadeep Das <[email protected]>

Examples

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exclude <- list(0,c(1,9))

int_PCA <- integrate_pca(Assays = c("H2az",
"H3k9ac"), name = multi_assay, mergetype = 2,
exclude = exclude, groupinfo = groupinfo_ext,
,graph = FALSE)

name = int_PCA$int_PCA


plot_integrated_density_3D(name = name, PC1 = 1, PC2 = 2,
group = c("WE","RE"), gridsize = 100, static = FALSE,
groupinfo = groupinfo_ext)

subhadeep1024/OMICsPCA documentation built on Sept. 30, 2018, 1 p.m.