showClusterHeatmap

Creates heatmap based on identified clusters

showClusterHeatmap(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes = "all",
  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

gobject

giotto object

expression_values

expression values to use

genes

vector of genes to use, default to 'all'

cluster_column

name of column to use for clusters

cor

correlation score to calculate distance

distance

distance method to use for hierarchical clustering

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 the Heatmap function from ComplexHeatmap

Value

ggplot

Details

Correlation heatmap of selected clusters.

Examples

data(mini_giotto_single_cell)
#> Warning: data set ‘mini_giotto_single_cell’ not found

# cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found

# create heatmap
showClusterHeatmap(mini_giotto_single_cell,
                   cluster_column = 'cell_types')
#> Error: package 'ComplexHeatmap' is not yet installed
#> 
#>  To install:
#> if(!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager');
#> BiocManager::install(c("ComplexHeatmap"))