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Overview

We expect a snn_graph_cluster HDF5 group at the root of the file, containing details on the SNN graph-based clustering. The group itself should contain the parameters and results subgroups.

Definitions:

  • in_use: whether SNN graph clustering is the chosen method in choose_clustering.
  • num_cells: number of cells remaining after QC filtering.

Parameters

parameters will contain:

  • k: a scalar integer specifying the number of nearest neighbors to find.
  • scheme: a scalar string specifying the edge weighting scheme to use. This may be "rank", "number" or "jaccard".
  • resolution: a scalar float specifying the resolution of the multi-level community detection.

Results

If in_use = true, results should contain:

  • clusters: an integer dataset of length equal to num_cells, containing the SNN graph cluster assignment for each cell. For N clusters, there should be at least one occurrence of each integer in [0, N).

If in_use = false, clusters may be absent. If it is present, it should follow the constraints listed above.

History

Added in version 1.0.