geom_th_heatmap: Create heatmaps

In fionarhuang/TreeHeatmap: A package to plot heatmaps at different levels of a tree

Create heatmaps

Description

Create heatmaps

Usage

geom_th_heatmap(
  name = NULL,
  th_data = NULL,
  cluster_column = FALSE,
  hclust_method = "complete",
  dist_method = "euclidean",
  gap = 1,
  rel_width = 1,
  show_coltree = TRUE,
  gap_coltree = 0.5,
  rel_height_coltree = 0.1,
  color_coltree = "grey",
  size_coltree = 1,
  ...
)

Arguments

name	the name of the current heatmap
th_data	a matrix
cluster_column	a logical value, TRUE or FALSE. If TRUE, columns of the heatmap are rearranged according to their similarities.
hclust_method	the method used to do clustering. This should be "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid". See method for hclust.
dist_method	the method used to do clustering. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". See method for dist.
gap	a numeric value to specify the gap between the current and the previous heatmap
rel_width	a numeric value decide the relative width of the heatmap compared to the ggtree plot
show_coltree	TRUE or FALSE. If TRUE, the column tree is shown when cluster_column = TRUE
gap_coltree	a numeric value to decide the gap between the heatmap and the column tree
rel_height_coltree	the relative height of the column tree compared to the height of row tree.
color_coltree	the color of the column tree.
size_coltree	the line size of the column tree
...	Other arguments passed on to geom_tile to customize the heatmap.

Value

geom layer

Author(s)

Ruizhu Huang

fionarhuang/TreeHeatmap documentation built on Feb. 1, 2024, 7:30 a.m.