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