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CellGraphList Methods

CellGraphList-methods.Rd

Methods for CellGraphList objects. Subsetting, concatenation, and replacement type-check elements against CellGraph. Unloaded graphs may be stored as NULL; x[[i]] <- NULL keeps the name and stores NULL rather than dropping the element.

Usage

# S3 method for class 'CellGraphList'
print(x, ...)

# S3 method for class 'CellGraphList'
x[i, ...]

# S3 method for class 'CellGraphList'
x[i] <- value

# S3 method for class 'CellGraphList'
x[[i]] <- value

# S3 method for class 'CellGraphList'
names(x) <- value

# S3 method for class 'CellGraphList'
c(...)

# S3 method for class 'CellGraphList'
as.list(x, ...)

Arguments

x

A CellGraphList object

...

Currently not used

i

Index to extract or replace

value

A CellGraph, NULL, or a list of those

Value

[, [<-, [[<-, names<-, and c: a CellGraphList. as.list: a named list. print: x, invisibly.

Functions

  • print(CellGraphList): Print a CellGraphList

  • [: Subset a CellGraphList. Unknown character names raise an error.

  • `[`(CellGraphList) <- value: Replace a subset of graphs. NULL unloads the selected cells without dropping their names.

  • `[[`(CellGraphList) <- value: Replace a single graph. NULL unloads that cell without dropping its name.

  • names(CellGraphList) <- value: Set names. Names must be unique and non-missing.

  • c(CellGraphList): Concatenate CellGraphList objects with lists of CellGraph or NULL. A bare CellGraph uses the argument name, or CellGraph1, CellGraph2, ... when unnamed.

  • as.list(CellGraphList): Convert to a named list

See also

CellGraphList

Examples

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

edges <- tibble(from = c("a", "b"), to = c("b", "c"))
g <- as_tbl_graph(edges, directed = FALSE) %N>%
  mutate(node_type = c("umi1", "umi2", "umi1"))
attr(g, "type") <- "bipartite"
cg <- CreateCellGraphObject(cellgraph = g)
cgl <- CreateCellGraphList(list(cell_1 = cg, cell_2 = cg))

# Print and subset
print(cgl)
#> A CellGraphList with 2 loaded CellGraph object(s) out of 2 
#> Names: cell_1, cell_2  
cgl[1]
#> A CellGraphList with 1 loaded CellGraph object(s) out of 1 
#> Names: cell_1  

# Unload a graph without dropping its name
cgl[[1]] <- NULL

# Concatenate while keeping the class
c(cgl[1], cgl[2])
#> A CellGraphList with 1 loaded CellGraph object(s) out of 2 
#> Names: cell_1, cell_2