Adding graph managing to SpatialExperiment

Dario Righelli

Leader(s)

Difficulty & duration

  • intermediate
  • a week

Abstract

Molecule-based spatial data requires to build graph based data representation. Indeed, some packages already are developing methods for iGraph analysis, miloR is for differential abundance in on KNN graph from single-cell datasets.

SingleCellExperiment has colPairs, whose purpose is to store networks consistent with stored colnames in the object.

Open questions:

  • is the iGraph the best solution for achieve this scope?
  • is this representation useful also in spot-based sptaial data?
  • could this graph representation be related with polygon representation of the cells?

Targets

  • integrate graph data structure into SpatialExperiment package (if needed)
  • add methods for managing this data structure