hclust_and_heat: Hierarchical Clustering & visualization by heatmap

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Hierarchical Clustering & visualization by heatmap

Description

Hierarchical cluster analysis and visualization by ezlimmaplot ezheat.

Usage

hclust_and_heat(
  object,
  annot,
  sc = c("z", "ctr", "none"),
  clip = NA,
  dist.method = "euclidean",
  hc.method = "ward.D2",
  deepSplit = 1,
  minClusterSize = 10,
  verbose = TRUE,
  pheno.df = NULL,
  labrows = "",
  labcols = "",
  color.v = NULL,
  annotation_colors = NULL,
  main = "Log2 Expression",
  name = "hclust_heat",
  reorder_cols = FALSE,
  gaps_col = NULL,
  width = NA,
  height = NA,
  plot = TRUE
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
annot	Feature annotation.
sc	Row scaling. Should rows be centered ('ctr'), z-scored ('z'), or neither ('none').
clip	Values with magnitude > clip are reset to value clip. If given, must be > 0.
dist.method	The distance measure to be used.
hc.method	The agglomeration method to be used.
deepSplit	For method "hybrid", can be either logical or integer in the range 0 to 4. For method "tree", must be logical. In both cases, provides a rough control over sensitivity to cluster splitting. The higher the value (or if TRUE), the more and smaller clusters will be produced. For the "hybrid" method, a finer control can be achieved via maxCoreScatter and minGap below.
minClusterSize	Minimum cluster size.
verbose	Logical; print pruning messages to console?
pheno.df	Data frame with rows as samples and columns as phenotypes.
labrows	Labels for rows, e.g. gene symbols. This can be of length 1 (in which case it is recycled), of length nrow(object).
labcols	Labels for columns. This can be of length 1 (in which case it is recycled), of length ncol(object).
color.v	Color palette for heatmap. If NULL, it's set to colorRampPalette(rev(brewer.pal(n=9, name='RdYlBu')))(50).
annotation_colors	list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. See pheatmap examples.
main	Main title of plot.
name	Name of file to create. Set to NA to plot to screen instead of to file.
reorder_cols	Logical; should columns be reordered with hierarchical clustering?
gaps_col	vector of column indices after which to insert gaps.
width	Manual option for determining the output file width in inches.
height	Manual option for determining the output file height in inches.
plot	Logical; should plot be generated?

Value

A data.frame of the clusters assignment and feature annotation.

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.