showClusterDendrogram#

Last Updated: Oct 02, 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