HCplot

Hierarchical clustering of samples from a precomputed beta-diversity matrix, plotted as a phylogram with tip labels colored by mmo$metadata$group.

Usage

HCplot(
  mmo,
  betadiv,
  outdir,
  hclust_method = "average",
  color = NULL,
  tip_label_size = 2.5,
  width = 10,
  height = 7,
  save_output = TRUE
)

Arguments

mmo

The mmo object

betadiv

Beta diversity distance matrix, output of GetBetaDiversity()

outdir

Output file prefix (e.g., "output/HC"). PNG saved here if save_output=TRUE.

hclust_method

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

color

Named vector of colors for groups. If NULL, uses Set3 palette.

tip_label_size

Tip label text size (default: 2.5)

width

Plot width in inches (default: 10)

height

Plot height in inches (default: 7)

save_output

Whether to save the plot (default: TRUE)

Value

A list containing: plot (ggplot object), hc (hclust), phy (phylo)

Examples

if (FALSE) {
bet <- GetBetaDiversity(mmo, method = 'bray', normalization = 'None')
hc <- HCplot(mmo, betadiv = bet, outdir = "output/HC_bray")
hc$plot
}