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

Description Usage Arguments Value Author(s) Examples

View source: R/analyse_integrated_variables.R

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

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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 <[email protected]>

Examples

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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)

subhadeep1024/OMICsPCA documentation built on Sept. 30, 2018, 1 p.m.