Create Average Metagene

createMetagenes()

This function creates an average metagene for gene clusters.

createMetagenes(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    gene_clusters,
    name = "metagene",
    return_gobject = TRUE
)

Arguments

gobject	Giotto object
expression_values	expression values to use
gene_clusters	numerical vector with genes as names
name	name of the metagene results
return_gobject	return giotto object

Value

Giotto object

Details

An example for the gene_clusters could be like this: cluster_vector = c(1, 1, 2, 2); names(cluster_vector) = c('geneA', 'geneB', 'geneC', 'geneD')

Examples

data(mini_giotto_single_cell)

# get all genes
all_genes = slot(mini_giotto_single_cell, 'gene_ID')

# create 2 metagenes from the first 6 genes
cluster_vector = c(1, 1, 1, 2, 2, 2) # 2 groups
names(cluster_vector) = all_genes[1:6]

mini_giotto_single_cell = createMetagenes(mini_giotto_single_cell,
                  gene_clusters = cluster_vector,
                  name = 'cluster_metagene')
#>
#>   cluster_metagene  has already been used, will be overwritten
# show metagene expression
spatCellPlot(mini_giotto_single_cell,
    spat_enr_names = 'cluster_metagene',
    cell_annotation_values = c('1', '2'),
    point_size = 3.5, cow_n_col = 2)