ht_clusters: Visualize the similarity matrix and the clustering. Adapted...

In scITD: Single-Cell Interpretable Tensor Decomposition

Visualize the similarity matrix and the clustering. Adapted from simplifyEnrichment package. https://github.com/jokergoo/simplifyEnrichment/blob/master/R/ht_clusters.R

Description

Visualize the similarity matrix and the clustering. Adapted from simplifyEnrichment package. https://github.com/jokergoo/simplifyEnrichment/blob/master/R/ht_clusters.R

Usage

ht_clusters(
  mat,
  cl,
  dend = NULL,
  col = c("white", "red"),
  draw_word_cloud = is_GO_id(rownames(mat)[1]) || !is.null(term),
  term = NULL,
  min_term = 5,
  order_by_size = FALSE,
  exclude_words = character(0),
  max_words = 10,
  word_cloud_grob_param = list(),
  fontsize_range = c(4, 16),
  column_title = NULL,
  ht_list = NULL,
  use_raster = TRUE,
  ...
)

Arguments

mat	A similarity matrix.
cl	Cluster labels inferred from the similarity matrix, e.g. from 'cluster_terms' or 'binary_cut'.
dend	Used internally.
col	A vector of colors that map from 0 to the 95^th percentile of the similarity values.
draw_word_cloud	Whether to draw the word clouds.
term	The full name or the description of the corresponding GO IDs.
min_term	Minimal number of functional terms in a cluster. All the clusters with size less than “min_term“ are all merged into one separated cluster in the heatmap.
order_by_size	Whether to reorder clusters by their sizes. The cluster that is merged from small clusters (size < “min_term“) is always put to the bottom of the heatmap.
exclude_words	Words that are excluded in the word cloud.
max_words	Maximal number of words visualized in the word cloud.
word_cloud_grob_param	A list of graphic parameters passed to 'word_cloud_grob'.
fontsize_range	The range of the font size. The value should be a numeric vector with length two. The minimal font size is mapped to word frequency value of 1 and the maximal font size is mapped to the maximal word frequency. The font size interlopation is linear.
column_title	Column title for the heatmap.
ht_list	A list of additional heatmaps added to the left of the similarity heatmap.
use_raster	Whether to write the heatmap as a raster image.
...	other parameters

Value

A list containing a 'ComplexHeatmap::HeatmapList-class' object and GO term ordering.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.