drcme.bin.run_joint_ephys_morph_tsne¶

Script to generate t-SNE coordinates using electrophysiology and morphological features.

The electrophysiology file is typically an sPCA value file. Both files should have normalized features (e.g., z-scored features). The two data sets can be weighted differently via the relative_ephys_weight parameter.

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

Parameter schema for joint t-SNE calculation

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

JointTsneParameters¶
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	Path to electrophysiology data file	NA	`InputFile`	str
morph_file	Path to morphology data file	NA	`InputFile`	str
output_file	Path to output file for t-SNE coordinates	NA	`OutputFile`	str
relative_ephys_weight	Relative weight of electrophysiology values (vs morphology values)	1.0	`Float`	float
perplexity	Perplexity parameter for t-SNE	25.0	`Float`	float
n_iter	Number of iterations for t-SNE	20000	`Integer`	int

Functions

main(ephys_file, morph_file, output_file, …)

Main runner function for script.

Classes

JointTsneParameters([extra, only, exclude, …])

Parameter schema for joint t-SNE calculation