Keep largest component — KeepLargestComponent • pixelatorR

Finds connected components of a graph and returns the largest component

Usage

KeepLargestComponent(object, ...)

# S3 method for tbl_graph
KeepLargestComponent(object, verbose = TRUE, ...)

# S3 method for CellGraph
KeepLargestComponent(object, verbose = TRUE, ...)

# S3 method for MPXAssay
KeepLargestComponent(object, verbose = TRUE, ...)

# S3 method for Seurat
KeepLargestComponent(object, assay = NULL, verbose = TRUE, ...)

Arguments

object: An object
...: Parameters passed to other methods
verbose: Print messages
assay: Name of a CellGraphAssay or CellGraphAssay5 assay stored on the Seurat object

Examples

library(pixelatorR)
library(tidygraph)

pxl_file <- system.file("extdata/five_cells",
                       "five_cells.pxl",
                       package = "pixelatorR")

# Read edgelist
edgelist <- ReadMPX_arrow_edgelist(pxl_file)
#> ℹ Extracting edgelist.parquet file to /var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/RtmpJCnvFY/edgelist.parquet
#> ✔ Returning FileSystemDataset

# Load graph from edge list and store in a CellGraph object
cg <- LoadCellGraphs(edgelist, cells = "RCVCMP0000217")[[1]]
#> →   Loading 1 edgelist(s) as bipartite graph(s)
cg
#> A CellGraph object containing a bipartite graph with 2470 nodes and 5138 edges
#> Number of markers:  79 

# Fetch tbl_graph from CellGraph object
g <- CellGraphData(cg, slot = "cellgraph")
g
#> # A tbl_graph: 2470 nodes and 5138 edges
#> #
#> # An undirected simple graph with 1 component
#> #
#> # Node Data: 2,470 × 2 (active)
#>    name                        node_type
#>    <chr>                       <chr>    
#>  1 GGTATATATTTTAAGTAGTTTAGTA-A A        
#>  2 ATTATGTTGTTGTATGTTTATTATT-A A        
#>  3 TCCGTGGTTTGATACTCGGGAATTT-A A        
#>  4 AGTGTAAGAGGTTGTTTCTTAGAAA-A A        
#>  5 GAGCAGACAATGGCGCTTAGCTAAA-A A        
#>  6 CAATTTTGACCTAGTTGTGGCCAAG-A A        
#>  7 ATGTCAGAGTGAATAGTTGTGATTG-A A        
#>  8 ATAAAGTGACCAGTTGAATGGGCCC-A A        
#>  9 TGCCTCTTGAGCTGTTGATCGCCTG-A A        
#> 10 ATTAGATGTAGAGCGCGAAAATTGG-A A        
#> # ℹ 2,460 more rows
#> #
#> # Edge Data: 5,138 × 2
#>    from    to
#>   <int> <int>
#> 1     1  1396
#> 2     1  1599
#> 3     1  1734
#> # ℹ 5,135 more rows

# Break graph by removing random edges
set.seed(132)
g <- g %E>%
 filter(from %in% sample(from, n() - 500))

# Fetch largest component from a tbl_graph
g_largest <- KeepLargestComponent(g)
#> ℹ Removed 35 out of 2470 nodes
g_largest
#> # A tbl_graph: 2435 nodes and 5103 edges
#> #
#> # An undirected simple graph with 1 component
#> #
#> # Node Data: 2,435 × 2 (active)
#>    name                        node_type
#>    <chr>                       <chr>    
#>  1 GGTATATATTTTAAGTAGTTTAGTA-A A        
#>  2 ATTATGTTGTTGTATGTTTATTATT-A A        
#>  3 TCCGTGGTTTGATACTCGGGAATTT-A A        
#>  4 AGTGTAAGAGGTTGTTTCTTAGAAA-A A        
#>  5 GAGCAGACAATGGCGCTTAGCTAAA-A A        
#>  6 CAATTTTGACCTAGTTGTGGCCAAG-A A        
#>  7 ATGTCAGAGTGAATAGTTGTGATTG-A A        
#>  8 ATAAAGTGACCAGTTGAATGGGCCC-A A        
#>  9 TGCCTCTTGAGCTGTTGATCGCCTG-A A        
#> 10 ATTAGATGTAGAGCGCGAAAATTGG-A A        
#> # ℹ 2,425 more rows
#> #
#> # Edge Data: 5,103 × 2
#>    from    to
#>   <int> <int>
#> 1     1  1362
#> 2     1  1565
#> 3     1  1700
#> # ℹ 5,100 more rows

# Add new graph to CellGraph object
cg@cellgraph <- g_largest

# Fetch largest component from a CellGraph
cg_largest <- KeepLargestComponent(cg)
#> ℹ Graph is already connected
cg_largest
#> A CellGraph object containing a bipartite graph with 2435 nodes and 5103 edges
#> Number of markers:  79