CellGraphs

Get and set CellGraph lists for different objects.

Usage

CellGraphs(object, ...)

CellGraphs(object, ...) <- value

# S3 method for MPXAssay
CellGraphs(object, ...)

# S3 method for MPXAssay
CellGraphs(object, ...) <- value

# S3 method for Seurat
CellGraphs(object, ...)

# S3 method for Seurat
CellGraphs(object, ...) <- value

Arguments

object

A Seurat, CellGraphAssay or CellGraphAssay object

...

Arguments passed to other methods

value

A list of CellGraph objects

Value

Returns a list of CellGraph objects. If there are no CellGraph objects present, returns an empty named list.

See also

PolarizationScores() and ColocalizationScores() for getting/setting spatial metrics

Examples

library(pixelatorR)
library(dplyr)
library(tidygraph)

pxl_file <- system.file("extdata/five_cells",
                        "five_cells.pxl",
                        package = "pixelatorR")
counts <- ReadMPX_counts(pxl_file)
#> ℹ Loading count data from /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/RtmpMJapOH/temp_libpatha88241f348a/pixelatorR/extdata/five_cells/five_cells.pxl
edgelist <- ReadMPX_item(pxl_file, items = "edgelist")
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/RtmpMJapOH/temp_libpatha88241f348a/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading edgelist data
#> ✔ Returning a 'tbl_df' object
components <- colnames(counts)
edgelist_split <-
  edgelist %>%
  select(upia, upib, component) %>%
  distinct() %>%
  group_by(component) %>%
  group_split() %>%
  setNames(nm = components)

# Convert data into a list of CellGraph objects
bipartite_graphs <- lapply(edgelist_split, function(x) {
  x <- x %>% as_tbl_graph(directed = FALSE)
  x <- x %>% mutate(node_type = case_when(name %in% edgelist$upia ~ "A", TRUE ~ "B"))
  attr(x, "type") <- "bipartite"
  CreateCellGraphObject(cellgraph = x)
})

# CellGraphs getter CellGraphAssay
# ---------------------------------

# Create CellGraphAssay
cg_assay <- CreateCellGraphAssay(counts = counts, cellgraphs = bipartite_graphs)
cg_assay
#> CellGraphAssay data with 80 features for 5 cells
#> First 10 features:
#>  CD274, CD44, CD25, CD279, CD41, HLA-ABC, CD54, CD26, CD27, CD38 
#> Loaded CellGraph objects:
#>  5

# Get cellgraphs from a CellGraphAssay object
CellGraphs(cg_assay)
#> $RCVCMP0000217
#> A CellGraph object containing a bipartite graph with 3507 nodes and 7580 edges
#> 
#> $RCVCMP0000118
#> A CellGraph object containing a bipartite graph with 2470 nodes and 5138 edges
#> 
#> $RCVCMP0000487
#> A CellGraph object containing a bipartite graph with 4225 nodes and 8150 edges
#> 
#> $RCVCMP0000655
#> A CellGraph object containing a bipartite graph with 4340 nodes and 9918 edges
#> 
#> $RCVCMP0000263
#> A CellGraph object containing a bipartite graph with 2258 nodes and 4303 edges
#> 


# CellGraphs setter CellGraphAssay
# ---------------------------------

# Set cellgraphs in a CellGraphAssay object
CellGraphs(cg_assay) <- cg_assay@cellgraphs


# CellGraphs getter Seurat
# ---------------------------------
se <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins

# Get cellgraphs from a Seurat object
CellGraphs(se)
#> $RCVCMP0000217
#> NULL
#> 
#> $RCVCMP0000118
#> NULL
#> 
#> $RCVCMP0000487
#> NULL
#> 
#> $RCVCMP0000655
#> NULL
#> 
#> $RCVCMP0000263
#> NULL
#> 


# CellGraphs setter Seurat
# ---------------------------------

# Set cellgraphs in a Seurat object
CellGraphs(se) <- cg_assay@cellgraphs