ht_clusters {scITD}

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.