addGenesPerc — addGenesPerc • Giotto

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

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)
#>      cell_ID nr_genes perc_genes total_expr leiden_clus cell_types
#>  1:   cell_2       13         65  111.98320           3     cell C
#>  2:   cell_7       15         75  115.73030           3     cell C
#>  3:  cell_12       11         55   95.49802           1     cell A
#>  4:  cell_15       12         60   99.94782           3     cell C
#>  5:  cell_17       13         65  111.32963           2     cell B
#>  6:  cell_30       11         55   96.64302           3     cell C
#>  7:  cell_37        6         30   57.77777           2     cell B
#>  8:  cell_40        9         45   82.84693           2     cell B
#>  9:  cell_44        9         45   79.93838           2     cell B
#> 10:  cell_53        9         45   82.40747           1     cell A
#> 11:  cell_64        8         40   73.06345           1     cell A
#> 12:  cell_74       11         55   93.04295           3     cell C
#> 13:  cell_85        8         40   73.72574           1     cell A
#> 14:  cell_86       14         70  115.75186           1     cell A
#> 15:  cell_90       11         55   93.02181           1     cell A
#> 16:  cell_95        6         30   59.55714           1     cell A
#> 17:  cell_96       10         50   88.31757           1     cell A
#> 18: cell_107       16         80  130.62640           1     cell A
#> 19: cell_113       12         60   99.83100           2     cell B
#> 20: cell_118       14         70  117.63523           2     cell B
#>     random_gene_perc
#>  1:            30.48
#>  2:            27.45
#>  3:            34.39
#>  4:            18.85
#>  5:            32.21
#>  6:            27.41
#>  7:            32.67
#>  8:            35.34
#>  9:            33.15
#> 10:            33.61
#> 11:            34.85
#> 12:            17.96
#> 13:            14.80
#> 14:            26.70
#> 15:            20.29
#> 16:            15.27
#> 17:            18.97
#> 18:            24.87
#> 19:            34.30
#> 20:            29.58