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CellGraph Methods

CellGraph-methods.Rd

Methods for CellGraph objects for generics defined in other packages

Usage

# S3 method for class 'CellGraph'
Layers(object, search = NULL, ...)

# S3 method for class 'CellGraph'
LayerData(object, layer = "counts", ...)

# S3 method for class 'CellGraph'
LayerData(object, layer = "counts", ...) <- value

# S3 method for class 'CellGraph'
Embeddings(object, reduction = NULL, ...)

# S3 method for class 'CellGraph'
Loadings(object, reduction = NULL, ...)

# S3 method for class 'CellGraph'
Stdev(object, reduction = NULL, ...)

# S3 method for class 'CellGraph'
AddMetaData(object, metadata, col.name = NULL, ...)

# S3 method for class 'CellGraph'
FetchData(
  object,
  vars,
  cells = NULL,
  layer = NULL,
  clean = TRUE,
  add_marker = FALSE,
  ...
)

# S4 method for class 'CellGraph'
show(object)

# S4 method for class 'CellGraph,character,missing'
x[[i, j, ..., drop = TRUE]]

# S4 method for class 'CellGraph,character,missing,ANY'
x[[i, j, ...]] <- value

# S3 method for class 'CellGraph'
subset(x, nodes, ...)

# S3 method for class 'CellGraphList'
FetchData(
  object,
  vars,
  cells = NULL,
  layer = NULL,
  clean = FALSE,
  add_marker = FALSE,
  ...
)

Arguments

object

A CellGraph or CellGraphList object

Optional layer name or pattern passed to Layers

...

Currently not used

layer

Name of a node matrix layer. Use "counts" for the counts slot. For FetchData, NULL (default) selects "counts" when present, otherwise the first extra layer.

value

Replacement value

reduction

Name of a stored NodeDimReduc. Defaults to the first reduction when NULL.

metadata

A vector, matrix, or data.frame of node metadata. Nodes are matched by name, so metadata may cover a subset of the graph; the remaining nodes get NA. Names that are not graph nodes are dropped.

col.name

Name of the metadata column when metadata is a vector

vars

Variables to fetch: marker names, node metadata columns, graph vertex attributes, or reduction embedding columns (for example "PC_1"). A variable missing from the graph (or from every cell in a list) aborts. A variable present on some cells in a list and missing on others is filled with NA and a warning names those cells.

cells

For FetchData.CellGraph, nodes to collect (default is all nodes). Numeric indices are allowed, matching FetchData. For FetchData.CellGraphList, component IDs (default is all loaded graphs). Unloaded graphs raise an error when they are included in cells.

clean

If TRUE, remove nodes that are missing data for every requested variable. FetchData.CellGraph defaults to TRUE. FetchData.CellGraphList defaults to FALSE so graphs that lack the requested variables still appear with NA values. A marker column added with add_marker is not treated as a requested variable.

add_marker

If TRUE, add a marker column with the marker label of each node from the one-hot counts matrix. Nodes with no count are NA. vars cannot include marker when this is TRUE.

x

A CellGraph object

i

Name of a stored reduction

j, drop

Required by the S4 [[ generic and ignored

nodes

A character vector of node names

Value

FetchData.CellGraph: a data.frame with nodes as rows and requested variables as columns. FetchData.CellGraphList: a data.frame with a component column identifying the source graph and the requested variables. Row names are node IDs and must be unique across the combined graphs. add_marker = TRUE also adds a marker column with the marker label of each node. subset: a CellGraph object containing only the specified nodes.

Details

Variable names must be unique across the graph node table, meta.data, reduction embeddings, and matrix features. Count and layer matrices may share feature names because layer selects the matrix to search.

Functions

  • FetchData(CellGraph): Pull node-level data from a CellGraph

  • show(CellGraph): Show a CellGraph object

  • x[[i: Extract a NodeDimReduc by name

  • `[[`(x = CellGraph, i = character, j = missing) <- value: Add or replace a NodeDimReduc

  • subset(CellGraph): Subset a CellGraph object

  • FetchData(CellGraphList): Pull node-level data from each loaded CellGraph in a CellGraphList. Unlike FetchLayoutData, this does not require a stored layout and does not reserve coordinate names, so vars may include x, y, or z when those columns exist on the graphs. component is reserved for the source graph ID. Node IDs are used as row names and must be unique across the graphs being combined. Variables missing from a graph are filled with NA and a warning names the cells that lacked the variable. Variables missing from every graph abort. Graphs that do not have a requested layer omit only features from that layer; metadata, vertex attributes, and reductions are kept. Remaining names are not looked up in counts or other layers. clean defaults to FALSE so those missing values are kept. add_marker = TRUE adds a marker column from the one-hot counts matrix of each graph.

Examples


library(pixelatorR)
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]]

# Show method
cg
#> A CellGraph object containing a bipartite graph with 43543 nodes and 97014 edges
#> Number of markers:  149 

# Fetch marker counts, node attributes, or embeddings
head(SeuratObject::FetchData(cg, vars = colnames(cg@counts)[1]))
#>                   B2M
#> 61208583141770358   0
#> 69733109123764664   0
#> 16002757515879905   0
#> 59822389138925142   0
#> 64270251753030037   0
#> 11111585952318758   0

# FetchData.CellGraphList combines loaded graphs without requiring a layout
cgl <- CellGraphs(se)
head(SeuratObject::FetchData(cgl, vars = colnames(cg@counts)[1]))
#>                          component B2M
#> 61208583141770358 0a45497c6bfbfb22   0
#> 69733109123764664 0a45497c6bfbfb22   0
#> 16002757515879905 0a45497c6bfbfb22   0
#> 59822389138925142 0a45497c6bfbfb22   0
#> 64270251753030037 0a45497c6bfbfb22   0
#> 11111585952318758 0a45497c6bfbfb22   0

# Subset
cg_small <- subset(cg, nodes = CellGraphData(cg, slot = "nodes")[1:100])
cg_small
#> A CellGraph object containing a bipartite graph with 100 nodes and 0 edges
#> Number of markers:  149