showClusterDendrogram: showClusterDendrogram

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Creates dendrogram for selected clusters.

Usage

showClusterDendrogram(
  gobject,
  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
expression_values	expression values to use
cluster_column	name of column to use for clusters
cor	correlation score to calculate distance
distance	distance method to use for hierarchical clustering
h	height of horizontal lines to plot
h_color	color of horizontal lines
rotate	rotate dendrogram 90 degrees
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
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 for ggdendrogram()

Details

Expression correlation dendrogram for selected clusters.

Value

ggplot

Examples

    showClusterDendrogram(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.