plot_integrated_density {OMICsPCA} | R Documentation

## Visualization of Density of various groups on Principal components of integrated assays

### 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 <subhadeep1024@gmail.com>

### 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

[Package OMICsPCA version 1.10.0 Index]