showClusterDendrogram#

Last Updated: Jan 29, 2024

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