plot_integrated_density: Visualization of 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 works similarly as "plot_density()". See the man page of "plot_density()" for details.

Usage

plot_integrated_density(name, PC = 1, groups,
groupinfo = NULL, ...)

Arguments

name	Name of the integrated "PCA"" object
PC	A number corresponding to the principal component on which density is to be calculated. default = 1
groups	A vector of names or subset of names of groups
groupinfo	same as plot_density()
...	additional arguments allowed to base function "geom_density" of package "ggplot2"

Value

a "gg" "ggplot" object

Author(s)

Subhadeep Das <[e-mail]>

Examples

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

densityplot <- plot_integrated_density(name = name, PC = 1,
groups = c("WE","RE","IntE","NE"), groupinfo = groupinfo_ext)

# additional graphical functions (e.g. xlim, ylim, theme) may be
#added with densityplot (see section VIII. Density analysis)

densityplot

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