Process and filter a Giotto object

library(Giotto)

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1. create Giotto object

path_to_matrix = system.file("extdata", "seqfish_field_expr.txt", package = 'Giotto')
path_to_locations = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto')

my_giotto_object = createGiottoObject(raw_exprs = path_to_matrix,
                                      spatial_locs = path_to_locations)

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2. filter Giotto object based on gene and cell coverage

my_giotto_object <- filterGiotto(gobject = my_giotto_object, 
                                 expression_threshold = 1, 
                                 gene_det_in_min_cells = 10, 
                                 min_det_genes_per_cell = 5)

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3. normalize Giotto object

my_giotto_object <- normalizeGiotto(gobject = my_giotto_object, scalefactor = 6000, verbose = T)

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4. (optional) add gene and cell statistics and adjust matrix for technical covariates or batch effects

my_giotto_object <- addStatistics(gobject = my_giotto_object)
my_giotto_object <- adjustGiottoMatrix(gobject = my_giotto_object, 
                                       expression_values = c('normalized'),
                                       covariate_columns = c('nr_genes', 'total_expr'))