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

# get all genes
all_genes = slot(mini_giotto_single_cell, 'gene_ID')
#> Error: object 'mini_giotto_single_cell' not found

# 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]
#> Error: object 'all_genes' not found

mini_giotto_single_cell = createMetagenes(mini_giotto_single_cell,
                                          gene_clusters = cluster_vector,
                                          name = 'cluster_metagene')
#> Error in createMetagenes(mini_giotto_single_cell, gene_clusters = cluster_vector,     name = "cluster_metagene"): could not find function "createMetagenes"

# 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)
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found