Get and set CellGraph object data

Usage

CellGraphData(object, slot = "cellgraph")

CellGraphData(object, slot = "cellgraph") <- value

Arguments

object: A CellGraph object
slot: Information to pull from object (cellgraph, counts, layout, layers, meta.data, reductions). meta_data is accepted as an alias for meta.data.
value: A new variable to place in slot

Value

GetCellGraphData: A CellGraph object slot

CellGraphData<-: A CellGraph with updated data

Examples


library(pixelatorR)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
library(tidygraph)
#> 
#> Attaching package: ‘tidygraph’
#> The following object is masked from ‘package:stats’:
#> 
#>     filter

se <- ReadPNA_Seurat(minimal_pna_pxl_file(), verbose = FALSE)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
se <- LoadCellGraphs(se, cells = colnames(se)[1], verbose = FALSE)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
cg <- CellGraphs(se)[[1]]

# Get slot data
CellGraphData(cg, slot = "cellgraph")
#> # A tbl_graph: 43543 nodes and 97014 edges
#> #
#> # An undirected simple graph with 1 component
#> #
#> # Node Data: 43,543 × 2 (active)
#>    name              node_type
#>    <chr>             <chr>    
#>  1 61208583141770358 umi1     
#>  2 69733109123764664 umi1     
#>  3 16002757515879905 umi1     
#>  4 59822389138925142 umi1     
#>  5 64270251753030037 umi1     
#>  6 11111585952318758 umi1     
#>  7 17475490163417931 umi1     
#>  8 68734019810858082 umi1     
#>  9 6353174121442465  umi1     
#> 10 21525916369122388 umi1     
#> # ℹ 43,533 more rows
#> #
#> # Edge Data: 97,014 × 2
#>    from    to
#>   <int> <int>
#> 1     1 18561
#> 2     2 18562
#> 3     3 18563
#> # ℹ 97,011 more rows

# Set slot data
CellGraphData(cg, slot = "cellgraph") <- CellGraphData(cg, slot = "cellgraph")