The SpatialCellData Class

Central S4 class for storing and analysing single-cell spatial biology data. Inspired by the Seurat object design, it holds raw and normalised marker intensities, spatial coordinates, cell-level metadata, and results from spatial analyses in a single container.

Slots

counts

Numeric matrix of raw marker intensities (cells x markers).

data

Numeric matrix of normalised marker intensities (cells x markers). Identical to counts until NormaliseData is called.

coords

Data frame with columns x and y holding spatial coordinates for each cell.

meta_data

Data frame of per-cell metadata. Always contains cell_id and sample_id. Additional columns such as cell_area, phenotype, or cluster are added by analysis functions.

project

Character string. Project or experiment name.

spatial

List for storing spatial analysis results (nearest-neighbour distances, density values, interaction matrices).