showClusterDendrogram

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 = NULL,
  return_plot = NULL,
  save_plot = NULL,
  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

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

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

...

Arguments passed on to ggdendro::ggdendrogram

data

Either a dendro object or an object that can be coerced to class dendro using the dendro_data() function, i.e. objects of class dendrogram, hclust or tree

segments

If TRUE, show line segments

labels

if TRUE, shows segment labels

leaf_labels

if TRUE, shows leaf labels

theme_dendro

if TRUE, applies a blank theme to plot (see theme_dendro())

Value

ggplot

Details

Expression correlation dendrogram for selected clusters.

Examples

g <- GiottoData::loadGiottoMini("visium", verbose = FALSE)
#> 
#> 1. use installGiottoEnvironment() to install
#>  a local miniconda python environment along with required modules
#> 
#> 2. provide an existing python path to
#>  python_path to use your own python path which has all modules
#>  installed
#> Set options("giotto.use_conda" = FALSE) if
#>  python functionalities are not needed
showClusterDendrogram(g, cluster_column = "leiden_clus")
#> Error: package 'ggdendro' is not yet installed
#> 
#>  To install:
#> install.packages(c("ggdendro"))