analyse_integrated_individuals: Quick analysis and visualization of the...

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

Description

This function works similarly as "analyse_individuals()". The only extra argument needs to be supplied here is "start_end", (if choice = 1.) returned by "integrate_pca()"

Usage

analyse_integrated_individuals(
name, choice = 1, geom = "point",
PC = c(1,2), groupinfo = NULL, ...)

Arguments

name	Name of the "PCA" object containing the integrated PCA.
choice	1 = 2D scatterplot on selected PCs through PC argument. 2 = 3D scatterplot on selected PCs through PC argument for details of the choices see the vignette
geom	Used when choice = 1. Avalilabe options are : "point", "text", c("point","text"). default = "point"
PC	A vector of numbers corresponding to principal components
groupinfo	same as integrate_variables()
...	additional arguments allowed to base function "plot3d" of package "rgl"

Value

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

Author(s)

Subhadeep Das <[e-mail]>

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

analyse_integrated_individuals(
name = name,
choice = 2, PC = c(1,2,3),
col = c("RED", "BLACK","GREEN"),
groupinfo = groupinfo_ext)

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