showClusterHeatmap

showClusterHeatmap

Description

Creates heatmap based on identified clusters

Usage

showClusterHeatmap(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes = "all",
  cluster_column,
  cor = c("pearson", "spearman"),
  distance = "ward.D",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "showClusterHeatmap",
  ...
)

Arguments

Argument	Description
gobject	giotto object
expression_values	expression values to use
genes	vector of genes to use, default to ‘all’
cluster_column	name of column to use for clusters
cor	correlation score to calculate distance
distance	distance method to use for hierarchical clustering
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
default_save_name	default save name for saving, don’t change, change save_name in save_param
...	additional parameters for the Heatmap function from ComplexHeatmap

Details

Correlation heatmap of selected clusters.

Value

ggplot

Examples

data(mini_giotto_single_cell)

# cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# create heatmap
showClusterHeatmap(mini_giotto_single_cell,
cluster_column = 'cell_types')