R/analyse_integrated_individuals.R

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

analyse_integrated_individuals <- function(
name, choice = 1, geom = "point",
PC = c(1,2), groupinfo = NULL, ...)
    {
        PCA <- name

        ordered_group <- groupinfo[match(
        rownames(PCA$ind$coord),rownames(groupinfo)),
        ,drop=FALSE]

        switch(choice,
                "1" = {
                        fviz_pca_ind(PCA,
                        geom.ind = geom, # show points only
                        col.ind = ordered_group$group, # color by groups,
                        axes = PC,
                        legend.title = "Groups", ...)
                },


                "2" = {

                  plot3d(PCA$ind$coord[,PC], xlab = paste0("PC",PC[1]),
                         ylab = paste0("PC",PC[2]),
                         zlab = paste0("PC",PC[3]), ...)
                }
    )

}