Spatial gene detection tools

1. processing steps

library(Giotto)

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)

# processing
my_giotto_object <- filterGiotto(gobject = seqfish_mini, 
                             expression_threshold = 0.5, 
                             gene_det_in_min_cells = 20, 
                             min_det_genes_per_cell = 0)
my_giotto_object <- normalizeGiotto(gobject = my_giotto_object)

# create network (required for binSpect methods)
my_giotto_object = createSpatialNetwork(gobject = my_giotto_object, minimum_k = 2)

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2. Run spatial gene detection methods

# binSpect kmeans method
km_spatialgenes = binSpect(my_giotto_object, bin_method = 'kmeans')

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = km_spatialgenes[1:2]$genes, point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)

# binSpect rank method
rnk_spatialgenes = binSpect(my_giotto_object, bin_method = 'rank')

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = rnk_spatialgenes[1:2]$genes, point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)

# silhouetteRank method
silh_spatialgenes = silhouetteRank(my_giotto_object)

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = silh_spatialgenes[1:2]$genes,  point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)

# spatialDE method
spatDE_spatialgenes = spatialDE(my_giotto_object)
results = data.table::as.data.table(spatDE_spatialgenes$results)
setorder(results, -LLR)

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = results$g[1:2],  point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)

# spark method
spark_spatialgenes = spark(my_giotto_object)
setorder(spark_spatialgenes, adjusted_pvalue, combined_pvalue)

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = spark_spatialgenes[1:2]$genes,  point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)

# trendsceek method
trendsc_spatialgenes = trendSceek(my_giotto_object)
trendsc_spatialgenes = data.table::as.data.table(trendsc_spatialgenes)

spatGenePlot(my_giotto_object, expression_values = 'scaled', 
             genes = trendsc_spatialgenes[1:2]$gene,  point_size = 3,
             point_shape = 'border', point_border_stroke = 0.1, cow_n_col = 2)