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
Details
Correlation heatmap of selected clusters.
Examples
data(mini_giotto_single_cell)
# cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)
# create heatmap
showClusterHeatmap(mini_giotto_single_cell,
cluster_column = 'cell_types')