The CellGraph class

The CellGraph class is designed to hold information needed for working with PNA single-cell graphs.

Details

A CellGraph contains counts and a graph, and optionally layouts, layers, metadata, or reductions.

Node-level variable names must be unique across the graph node table, meta.data, and reduction embeddings, and must not overlap count or layer features. Count and layer matrices are the exception: they may share feature names because callers select a layer explicitly.

Slots

cellgraph

A tbl_graph object corresponding to a cell graph

nodes

Character vector of node IDs in graph order. This is the map used to align counts, layouts, layers, metadata, and reductions. Those tables are stored in this order without copying the IDs as row names.

counts

A matrix-like object with marker counts (nodes x markers). Rows follow nodes. The counts matrix can be extracted as the "counts" layer via Layers / LayerData.

layout

A named list of data.frame objects with coordinates for cell layouts. Rows follow nodes. A name column or explicit row names are accepted on input and used only to reorder; MPX bipartite layouts may omit -A/-B suffixes. Stored layouts keep coordinate columns (typically x, y, z). Layouts without node IDs still work if the number of rows matches the graph.

layers

A named list of additional numeric node matrices (nodes x features), analogous to layers on a Seurat Assay5. A layer can be extracted via Layers / LayerData.

meta.data

A data.frame of node-level metadata (one row per node). Rows follow nodes. Columns may have mixed types.

reductions

A named list of NodeDimReduc objects