drcme.bin.run_ephys_morph_clustering¶

Script to cluster on combined electrophysiology and morphology data.

The script runs multiple clustering variants, determines consensus clusters, and finally evaluates the stability of each cluster.

class drcme.bin.run_ephys_morph_clustering.MeClusteringParameters(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)[source]¶

Parameter schema for electrophysiology/morphology clustering

This schema is designed to be a schema_type for an ArgSchemaParser object

MeClusteringParameters¶
key	description	default	field_type	json_type
input_json	file path of input json file	NA	`InputFile`	str
output_json	file path to output json file	NA	`OutputFile`	str
log_level	set the logging level of the module	ERROR	`LogLevel`	str
ephys_file	CSV file path with sparse PCA electrophysiology values	NA	`InputFile`	str
morph_file	CSV file path with morphology parameter values	NA	`InputFile`	str
weights	List of relative weights for the electrophysiology values	[1.0, 2.0, 4.0]	`List`	float
n_cl	List of number of clusters for initial clustering algorithms	[10, 15, 20, 25]	`List`	int
min_consensus_n	Minimum cluster size for consensus clusters	3	`Integer`	int
cocluster_matrix_file	Output file path for co-clustering matrix	NA	`OutputFile`	str
cluster_labels_file	Output file path for cluster labels	NA	`OutputFile`	str
specimen_id_file	Output file path for specimen IDs	NA	`OutputFile`	str
jaccards_file	Output file path for Jaccard coefficients	NA	`OutputFile`	str
ordering_file	Output file path for new cluster order	NA	`OutputFile`	str

Functions

main(ephys_file, morph_file, weights, n_cl, …)

Main runner function for script.

Classes

MeClusteringParameters([extra, only, …])

Parameter schema for electrophysiology/morphology clustering