analyse_variables: Quick analysis and visualization of the integrated Assays by...

In OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

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 <[e-mail]>

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)

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