Load edgelists
Edgelists.RdGet the edgelist(s) from a PNAAssay, PNAAssay5 or
a Seurat object. The edgelist(s) are stored on disk in the PXL files,
so the method only works if the paths are set correctly (see ?FSMap).
Usage
Edgelists(object, ...)
# S3 method for class 'PNAAssay'
Edgelists(object, lazy = TRUE, ...)
# S3 method for class 'PNAAssay5'
Edgelists(object, lazy = TRUE, ...)
# S3 method for class 'Seurat'
Edgelists(object, assay = NULL, meta_data_columns = NULL, lazy = TRUE, ...)Arguments
- object
An object with polarization scores
- ...
Not implemented
- lazy
A logical indicating whether to lazy load the edgelist(s) from the PXL files
- assay
Name of a
CellGraphAssay- meta_data_columns
A character vector with meta.data column names. This option can be useful to join meta.data columns with the proximity score table.
See also
Other spatial metrics:
ColocalizationScores(),
PolarizationScores(),
ProximityScores()
Examples
library(pixelatorR)
pxl_file <- minimal_pna_pxl_file()
seur_obj <- ReadPNA_Seurat(pxl_file)
#> ✔ Created a <Seurat> object with 5 cells and 158 targeted surface proteins
el <- Edgelists(seur_obj[["PNA"]], lazy = FALSE)
el
#> # A tibble: 528,594 × 7
#> marker_1 marker_2 umi1 umi2 read_count uei_count component
#> <chr> <chr> <int64> <int64> <int64> <int64> <chr>
#> 1 CD6 B2M 5.e16 8 e15 1 1 c3c393e9a17c1981
#> 2 CD6 B2M 2.e16 4 e16 3 3 c3c393e9a17c1981
#> 3 CD6 B2M 4 e16 6 e16 1 1 c3c393e9a17c1981
#> 4 CD6 B2M 6 e16 6 e16 1 1 c3c393e9a17c1981
#> 5 CD6 B2M 2.e16 6 e16 1 1 c3c393e9a17c1981
#> 6 CD6 B2M 1.e16 6 e16 1 1 c3c393e9a17c1981
#> 7 CD6 B2M 3 e16 5.e16 2 2 c3c393e9a17c1981
#> 8 CD6 B2M 6 e16 4 e16 1 1 c3c393e9a17c1981
#> 9 CD6 B2M 6 e16 5.e16 5 3 c3c393e9a17c1981
#> 10 CD6 B2M 4 e16 5.e16 1 1 c3c393e9a17c1981
#> # ℹ 528,584 more rows