clustheatmap: Plotting clusters in a heatmap representation of the cell...

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

Plotting clusters in a heatmap representation of the cell distances

Description

This functions plots a heatmap of the distance matrix grouped by clusters. Individual clusters are highlighted with rainbow colors along the x and y-axes.

Usage

clustheatmap(
  object,
  clustering_method = "k-means",
  hmethod = "single",
  rseed = NULL,
  quiet = FALSE,
  plot = TRUE
)

## S4 method for signature 'DISCBIO'
clustheatmap(
  object,
  clustering_method = "k-means",
  hmethod = "single",
  rseed = NULL,
  quiet = FALSE,
  plot = TRUE
)

Arguments

object	DISCBIO class object.
clustering_method	either "k-means" or "model-based" ("k" and "mb" are also accepted)
hmethod	Agglomeration method used for determining the cluster order from hierarchical clustering of the cluster medoids. This should be one of "ward.D", "ward.D2", "single", "complete", "average". Default is "single".
rseed	Random integer to fix random results.
quiet	if 'TRUE', intermediary output is suppressed
plot	if 'TRUE', plots the heatmap; otherwise, just prints cclmo

Value

Unless otherwise specified, a heatmap and a vector of the underlying cluster order.

DIscBIO documentation built on Nov. 6, 2023, 5:08 p.m.