CellGraphAssay5 Methods

Methods for CellGraphAssay5 objects for generics defined in other packages

Join Layers Together

Usage

# S3 method for CellGraphAssay5
RenameCells(object, new.names = NULL, ...)

# S4 method for CellGraphAssay5
show(object)

# S3 method for CellGraphAssay5
subset(x, features = NULL, cells = NULL, ...)

# S3 method for CellGraphAssay5
merge(
  x = NULL,
  y = NULL,
  merge.data = TRUE,
  add.cell.ids = NULL,
  collapse = TRUE,
  ...
)

# S3 method for CellGraphAssay5
JoinLayers(object, layers = NULL, new = NULL, ...)

Arguments

object

A CelLGraphAssay5 object.

new.names

A character vector with new cell IDs. The length of the vector must be equal to the number of cells in the object and the names must be unique.

...

Additional arguments passed to other methods

x

A CellGraphAssay5 object

features

Feature names

cells

Cell names

y

A CellGraphAssay5 object or a list of CellGraphAssay5 objects

merge.data

Merge the data slots instead of just merging the counts (which requires renormalization); this is recommended if the same normalization approach was applied to all objects

add.cell.ids

A character vector with sample names

collapse

If TRUE, merge layers of the same name together

layers

A character vector of layer names to join.

new

Name of new layers

Value

A CelLGraphAssay5 object with layers joined

Functions

• RenameCells(CellGraphAssay5): Rename cell IDs of a CellGraphAssay5 object

• show(CellGraphAssay5): Show method for CellGraphAssay5 objects

• subset(CellGraphAssay5): Subset a CellGraphAssay5 object

• merge(CellGraphAssay5): Merge two or more CellGraphAssay5 objects together

• JoinLayers(CellGraphAssay5): Join layers

Examples

library(SeuratObject)
#> Loading required package: sp
#> ‘SeuratObject’ was built under R 4.3.2 but the current version is
#> 4.3.3; it is recomended that you reinstall ‘SeuratObject’ as the ABI
#> for R may have changed
#> 
#> Attaching package: ‘SeuratObject’
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, t
# Load example data as a Seurat object
pxl_file <- system.file("extdata/five_cells",
                        "five_cells.pxl",
                        package = "pixelatorR")
seur_obj <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins

# Merge Seurat objects
seur_obj_merged <- merge(seur_obj, seur_obj)
#> Warning: Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.
cg_assay <- seur_obj_merged[["mpxCells"]]

# The CellGraphAssay5 now has two count matrices
cg_assay
#> CellGraphAssay (v5) data with 80 features for 10 cells
#> Top 10 variable features:
#>  CD274, CD44, CD25, CD279, CD41, HLA-ABC, CD54, CD26, CD27, CD38 
#> Layers:
#>  counts.1, counts.2 
#> Loaded CellGraph objects:
#>  0

# Join layers
cg_assay <- JoinLayers(cg_assay)

# Now the CellGraphAssay5 has a single, merged count matrix
cg_assay
#> CellGraphAssay (v5) data with 80 features for 10 cells
#> Top 10 variable features:
#>  CD274, CD44, CD25, CD279, CD41, HLA-ABC, CD54, CD26, CD27, CD38 
#> Layers:
#>  counts 
#> Loaded CellGraph objects:
#>  0

# JoinLayers now also works on the Seurat object directly
seur_obj_merged <- JoinLayers(seur_obj_merged)
seur_obj_merged[["mpxCells"]]
#> CellGraphAssay (v5) data with 80 features for 10 cells
#> Top 10 variable features:
#>  CD274, CD44, CD25, CD279, CD41, HLA-ABC, CD54, CD26, CD27, CD38 
#> Layers:
#>  counts 
#> Loaded CellGraph objects:
#>  0