showClusterHeatmap: showClusterHeatmap

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

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

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
expression_values	expression values to use (e.g. "normalized", "scaled", "custom")
feats	vector of features to use, default to 'all'
genes	deprecated. Replaced by feats param
cluster_column	name of column to use for clusters (e.g. "leiden_clus")
cor	correlation score to calculate distance (e.g. "pearson", "spearman")
distance	distance method to use for hierarchical clustering, default to "ward.D"
show_plot	show plot. TRUE or FALSE
return_plot	return ggplot object. TRUE or FALSE
save_plot	directly save the plot. TRUE or FALSE
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don't change, change save_name in save_param
...	additional parameters passed to Heatmap function

Details

Correlation heatmap of selected clusters.

Value

ggplot

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.