`createMetagenes`¶

createMetagenes

Description¶

This function creates an average metagene for gene clusters.

Usage¶

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

Arguments¶

Argument	Description
`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

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’)

Value¶

giotto object

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')

# 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)