analyse_variables {OMICsPCA} | R Documentation

## Quick analysis and visualization of the integrated Assays by integrate() function.

### Description

This function is designed for a quick analysis and visualization of the data integrated by integrate() function. It takes 3 compulsory arguments name, Assay and choice. The type of analysis should be selected through the "choice" argument. This function acts as a wrapper around a collection of functions of package "factoextra" and "corrplot" and thus can take additional arguments specific and non-conflicting to such functions.

### Usage

    analyse_variables(name, Assay, choice, title = NULL, PC = 1,
    var_type = "contrib", ...)

### Arguments

`name` | Name of the "PCA" object
`Assay` | Name of an Assay.
`choice` |
    1 = variance barplot
    2 = Loadings of cell lines on selected PCs
    3 = hCorrelation matrix
    4 = Squarred loadings of Cell lines on a PC
    5 = Contribution of Cell lines on a PC

    for details of the choices see the vignette
`title` | Title of the plot. default = NULL
`PC` | used in choice = 4 and 5. Indicates the PC on which choice 4 and 5 will depend. default = 1
`var_type` | used in choice = 2. available options are: "coord", "cos2" and "contrib". default = "contrib"
`...` | extra arguments passed through the functions imported from various packages. See vignettes for details.

### Value

Displays various plots and tables as per the combination of input arguments

### Author(s)

Subhadeep Das <subhadeep1024@gmail.com>

### Examples

    PCAlist <- integrate_variables(Assays = c("H2az","H3k4me1",
    "H3k9ac"), name = multi_assay,
    groups = c("WE","RE"), groupinfo = groupinfo_ext,
    scale.unit = FALSE, graph = FALSE)

    analyse_variables(name = PCAlist, Assay = "H2az", choice = 1,
    title = "variance barplot", addlabels = TRUE)

[Package OMICsPCA version 1.4.0 Index]