cluster cells using a NN-network and the Leiden community detection algorithm
doLeidenCluster( gobject, name = "leiden_clus", nn_network_to_use = "sNN", network_name = "sNN.pca", python_path = NULL, resolution = 1, weight_col = "weight", partition_type = c("RBConfigurationVertexPartition", "ModularityVertexPartition"), init_membership = NULL, n_iterations = 1000, return_gobject = TRUE, set_seed = T, seed_number = 1234 )
| gobject | giotto object |
|---|---|
| name | name for cluster |
| nn_network_to_use | type of NN network to use (kNN vs sNN) |
| network_name | name of NN network to use |
| python_path | specify specific path to python if required |
| resolution | resolution |
| weight_col | weight column to use for edges |
| partition_type | The type of partition to use for optimisation. |
| init_membership | initial membership of cells for the partition |
| n_iterations | number of interations to run the Leiden algorithm. If the number of iterations is negative, the Leiden algorithm is run until an iteration in which there was no improvement. |
| return_gobject | boolean: return giotto object (default = TRUE) |
| set_seed | set seed |
| seed_number | number for seed |
giotto object with new clusters appended to cell metadata
This function is a wrapper for the Leiden algorithm implemented in python, which can detect communities in graphs of millions of nodes (cells), as long as they can fit in memory. See the https://github.com/vtraag/leidenalgleidenalg github page or the https://leidenalg.readthedocs.io/en/stable/index.htmlreadthedocs page for more information.
Partition types available and information:
RBConfigurationVertexPartition: Implements Reichardt and Bornholdt’s Potts model with a configuration null model. This quality function is well-defined only for positive edge weights. This quality function uses a linear resolution parameter.
ModularityVertexPartition: Implements modularity. This quality function is well-defined only for positive edge weights. It does not use the resolution parameter
Set weight_col = NULL to give equal weight (=1) to each edge.