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ColocalizationScores

ColocalizationScores.Rd

Get and set colocalization scores for a CellGraphAssay, CellGraphAssay5 or a Seurat object

Usage

ColocalizationScores(object, ...)

ColocalizationScores(object, ...) <- value

# S3 method for class 'MPXAssay'
ColocalizationScores(object, add_marker_counts = FALSE, ...)

# S3 method for class 'MPXAssay'
ColocalizationScores(object, ...) <- value

# S3 method for class 'Seurat'
ColocalizationScores(
  object,
  assay = NULL,
  meta_data_columns = NULL,
  add_marker_counts = FALSE,
  ...
)

# S3 method for class 'Seurat'
ColocalizationScores(object, assay = NULL, ...) <- value

Arguments

object

An object with polarization scores

...

Not implemented

value

A tbl_df with colocalization scores

add_marker_counts

A logical value indicating whether to add marker counts to the colocalization score table.

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 colocalization score table.

Value

ColocalizationScores: Colocalization scores

ColocalizationScores<-: An object with colocalization scores updated

See also

Other spatial metrics: Edgelists(), PolarizationScores(), ProximityScores()