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#
|
giotto object |
|
spatial unit (e.g. “cell”) |
|
feature type (e.g. “rna”, “dna”, “protein”) |
|
expression values to use (e.g. “normalized”, “scaled”, “custom”) |
|
name of column to use for clusters (e.g. “leiden_clus”) |
|
correlation score to calculate distance (e.g. “pearson”, “spearman”) |
|
distance method to use for hierarchical clustering, default to “ward.D” |
|
height of horizontal lines to plot |
|
color of horizontal lines |
|
rotate dendrogram 90 degrees |
|
show plot. TRUE or FALSE |
|
return ggplot object. TRUE or FALSE |
|
directly save the plot. TRUE or FALSE |
|
list of saving parameters, see
|
|
default save name for saving, don’t change, change save_name in save_param |
|
additional parameters passed to
|
Details#
Expression correlation dendrogram for selected clusters.
Value#
ggplot