Create Cluster Heatmap

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

A ggplot value.

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')