showClusterHeatmap

showClusterHeatmap

Description

Creates heatmap based on identified clusters

Usage

showClusterHeatmap(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats = "all",
  genes = NULL,
  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

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

feats

vector of features to use, default to ‘all’

genes

deprecated. Replaced by feats param

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