analyse_integrated_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 "integrateAssays()"" function. It works similarly as analyse_variables. In addition to that it takes an additinal argument "start_end" returned by "integrateAssays()".

### Usage

    analyse_integrated_variables(start_end = start_end, Assay = "all",
    name, choice, title = NULL, PC = 1,
    var_type = "contrib", ...)

### Arguments

`start_end` | a list as returned by "integrate_pca()"
`Assay` | Name of an Assay. default = "all"
`name` | Name of the "PCA" object returned by "integrate_pca()"
`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 plots
`PC` | The PC on which the plots will be drawn. used in choice 4 and 5. default = 1
`var_type` | Used when choice = 2. available options are: "coord", "cos2" and "contrib"
`...` | additional arguments allowed to base functions "used in various choices. 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

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

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

    start_end = int_PCA$start_end

    name = int_PCA$int_PCA

    analyse_integrated_variables(start_end = start_end, name = name,
    choice = 1, title = "variance barplot", Assay = 1, addlabels = TRUE)

[Package OMICsPCA version 1.10.0 Index]