analyse_variables {OMICsPCA} | R Documentation |
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.
analyse_variables(name, Assay, choice, title = NULL, PC = 1, var_type = "contrib", ...)
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. |
Displays various plots and tables as per the combination of input arguments
Subhadeep Das <subhadeep1024@gmail.com>
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)