Plot_PCoA: Stratified PCoA plots

In wdl2459/ConQuR: Batch Effects Removal for Microbiome Data in Large-Scale Epidemiology Studies via Conditional Quantile Regression

Stratified PCoA plots

Description

Stratified PCoA plots

Usage

Plot_PCoA(
  TAX,
  factor,
  sub_index = NULL,
  dissimilarity = "Bray",
  GUniFrac_type = "d_0.5",
  tree = NULL,
  main = NULL,
  aa = 1.5
)

Arguments

TAX	The taxa read count table, samples (row) by taxa (col).
factor	The variable for stratification, e.g., batchid or the variable of interest, must be a factor.
sub_index	A vector of sample indices, to restrict the analysis to a subgroup of samples, e.g., c(1:5, 15:20); default is NULL.
dissimilarity	The dissimilarity type, “Bray” for Bray-Curtis dissimilarity, “Aitch” for Aitchison dissimilarity, “GUniFrac” for generalized UniFrac dissimilarity; default is “Bray”.
GUniFrac_type	The generalized UniFrac type, “d_1” for weighted UniFrac, “d_UW” for unweighted UniFrac, “d_VAW” for variance adjusted weighted UniFrac, “d_0” for generalized UniFrac with alpha 0, “d_0.5” for generalized UniFrac with alpha 0.5; default is “d_0.5”.
tree	The rooted phylogenetic tree of R class “phylo”, must be provided when dissimilarity=“GUniFrac”; default is NULL.
main	The title of plot; default is NULL.
aa	A real number, the character size for the title.

Value

Print a PCoA plot.

References

• Chen, J., & Chen, M. J. (2018). Package ‘GUniFrac’. The Comprehensive R Archive Network (CRAN).

wdl2459/ConQuR documentation built on Aug. 28, 2022, 6:08 a.m.