The binned matrix stored in a STGrid object

bin_mat(
  object,
  as_factor = FALSE,
  feat_list = character(),
  melt_tab = FALSE,
  del_bin = FALSE,
  pseudo_count = 0,
  transform = c("None", "log2", "log10", "log"),
  axis_as_number = FALSE
)

Arguments

object: The STGrid object
as_factor: Should bin_x and bin_y columns be returned as ordered factor ?
feat_list: Whether to subset to some features.
melt_tab: Whether to melt.
del_bin: Whether to delete the bin_x, bin_y columns.
pseudo_count: Whether to add a pseudo_count.
transform: Whether the count should be transformed.
axis_as_number: If melt_tab is TRUE, whether bin_x and bin_y should be transformed to numerics.

Examples

example_dataset()
#> |-- INFO :  Dataset 11284233/files/Xenium_Mouse_Brain_Coronal_7g was already loaded. 
head(bin_mat(Xenium_Mouse_Brain_Coronal_7g))
#>                                             bin_x     bin_y Ano1 Chat Ebf3
#> [1.01e+03,1.03e+03)~[22,47)   [1.01e+03,1.03e+03)   [22,47)    0    0    0
#> [1.01e+03,1.03e+03)~[47,72)   [1.01e+03,1.03e+03)   [47,72)    0    0    0
#> [1.01e+03,1.03e+03)~[72,97)   [1.01e+03,1.03e+03)   [72,97)    0    0    0
#> [1.01e+03,1.03e+03)~[97,122)  [1.01e+03,1.03e+03)  [97,122)    0    0    0
#> [1.01e+03,1.03e+03)~[122,147) [1.01e+03,1.03e+03) [122,147)    0    0    0
#> [1.01e+03,1.03e+03)~[147,172) [1.01e+03,1.03e+03) [147,172)    0    0    0
#>                               Kctd8 Necab2 Nrp2 Nwd2
#> [1.01e+03,1.03e+03)~[22,47)       0      0    0    0
#> [1.01e+03,1.03e+03)~[47,72)       0      0    0    0
#> [1.01e+03,1.03e+03)~[72,97)       0      0    0    0
#> [1.01e+03,1.03e+03)~[97,122)      0      0    0    0
#> [1.01e+03,1.03e+03)~[122,147)     0      0    0    0
#> [1.01e+03,1.03e+03)~[147,172)     0      0    0    0