HCplot

Hierarchical clustering of samples from a precomputed beta-diversity matrix and plotting as a phylogram with tip labels colored by species (or any grouping column).

Usage

HCplot(
  mmo,
  betadiv,
  outdir,
  group_col = "Species_binomial",
  sample_col = "sample",
  hclust_method = "average",
  palette = "Dark 3",
  cex = 0.6,
  width = 10,
  height = 7,
  save_output = TRUE
)

Arguments

mmo

The mmo object containing metadata in mmo$metadata

betadiv

The beta diversity distance matrix, output of GetBetaDiversity()

outdir

Output prefix for files (e.g., "output/HC"). If save_output=TRUE a PDF is saved.

group_col

Metadata column name used to color tips (default: "Species_binomial")

sample_col

Metadata column name containing sample IDs (default: "sample")

hclust_method

hclust linkage method (default: "average"; alternatives: "complete","ward.D2")

palette

Qualitative palette name for colorspace::qualitative_hcl (default: "Dark 3")

cex

Tip label size (default: 0.6)

width

PDF width (default: 10)

height

PDF height (default: 7)

save_output

Whether to save the plot to PDF (default: TRUE)

Value

A list containing: hc (hclust), phy (phylo), tip_df (mapping), colors (named palette)

Details

This function is intended for visualization (no cluster significance is implied).

Examples

if (FALSE) {
bet <- GetBetaDiversity(mmo, method='bray',
        normalization='Log', distance='dreams',
         filter_id=FALSE)
HCplot(mmo,
       betadiv = bet,
       outdir = "output/HC_dreams_bray")
}