showClusterDendrogram

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Last Updated: Mar 11, 2023

Description

Creates dendrogram for selected clusters.

Usage

showClusterDendrogram(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  cor = c("pearson", "spearman"),
  distance = "ward.D",
  h = NULL,
  h_color = "red",
  rotate = FALSE,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "showClusterDendrogram",
  ...
)

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”)
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”
h	height of horizontal lines to plot
h_color	color of horizontal lines
rotate	rotate dendrogram 90 degrees
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 ggdendrogram

Details

Expression correlation dendrogram for selected clusters.

Value

ggplot