showClusterHeatmap#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_visuals.R#L460

Description#

Creates heatmap based on identified clusters

Usage#

showClusterHeatmap(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats = "all",
  genes = NULL,
  cluster_column,
  cor = c("pearson", "spearman"),
  distance = "ward.D",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "showClusterHeatmap",
  ...
)

Arguments#

Argument

Description

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?)

feats

vector of features to use, default to ‘all’

genes

deprecated. Replaced by feats param

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?

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 `showSaveP arameters <#showsaveparameters>`__

default_save_name

default save name for saving, don’t change, change save_name in save_param

...

additional parameters passed to `Heatmap <#heatmap>`__ function

Details#

Correlation heatmap of selected clusters.

Value#

ggplot