addGenesPerc: addGenesPerc

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

calculates the total percentage of (normalized) counts for a subset of selected genes

Usage

addGenesPerc(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes = NULL,
  vector_name = "gene_perc",
  return_gobject = TRUE
)

Arguments

gobject	giotto object
expression_values	expression values to use
genes	vector of selected genes
vector_name	column name as seen in pDataDT()
return_gobject	boolean: return giotto object (default = TRUE)

Value

giotto object if return_gobject = TRUE, else a vector with

Examples

data(mini_giotto_single_cell)

# select genes (e.g. Rpl or mitochondrial)
random_genes = sample(slot(mini_giotto_single_cell, 'gene_ID'), 5)

# calculate percentage of those selected genes per cells/spot
updated_giotto_object = addGenesPerc(mini_giotto_single_cell,
                                     genes = random_genes,
                                     vector_name = 'random_gene_perc')

# visualize result in data.table format
pDataDT(updated_giotto_object)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.