Sample dendrogram

Hierarchically clusters the samples (columns of data.matrix) and writes a dendrogram to PDF; optionally also a phylogeny-style plot.

Usage

dendrogram_samples(
  data.matrix,
  hc_metric.var = "euclidean",
  hc_method.var = "ward.D2",
  type.var = NULL,
  output.dir = "results/figures/"
)

Arguments

data.matrix

Numeric matrix (features x samples).

hc_metric.var

Distance metric for clustering (e.g. "euclidean").

hc_method.var

Agglomeration method (e.g. "ward.D2").

type.var

Optional ape::plot.phylo() layout ("phylogram", "fan", "unrooted", "radial"); if NULL only the standard dendrogram is drawn.

output.dir

Directory to write the PDF(s) into (created if needed). Use NULL to skip writing.

Value

Invisibly, a list with the hclust object and the dendrogram plot.

Examples

if (FALSE) { # \dontrun{
dendrogram_samples(my_matrix, type.var = "unrooted")
} # }