R/jd_plot_ord.R

In jdwiyanto/mbiome: A convenient wrapper to visualise and run core analyses for multi-variable microbiome data

#' Ordinates metagenomic data based on variable(s)
#'
#' @param ps A phyloseq object
#' @param var a character string of the chosen variable. Must be one of the variables in sample_data(ps). Support multiple input variables
#' @param method Ordination plot used. Defaults to PCoA
#' @param distance A distance matrix for the ordination. Defaults to Euclidean
#' @export
jd_plot_ord <- function(ps, var, method = 'PCoA', distance ='euclidean') {

figlist = lapply(var, function(var) {
  sampledata = phyloseq::sample_data(ps)
  sampledata = subset(sampledata, !is.na(sampledata[[var]]))
  ps2 = phyloseq::phyloseq(sampledata, otu_table(ps), tax_table(ps))

  ord <- phyloseq::ordinate(ps2, method = method, distance = distance)

  fig <- phyloseq::plot_ordination(ps2, type = "samples", ordination = ord, color = var) +
         ggplot2::theme_bw() +
         ggsci::scale_color_igv(palette = 'default')

  return(fig)

})

if( var %>% length > 1 ) {
  fig = ggpubr::ggarrange(plotlist = figlist, labels = 'auto')
  return(fig)
} else {
  fig = ggpubr::ggarrange(plotlist = figlist)
  return(fig)
}
}