drcme.bin.run_combined_tsne¶

Script to generate t-SNE coordinates using two electrophysiology sPCA files.

The two files should be calculated using the same loadings. This is just a convenience script to merge the two data sets, run t-SNE, and save the coordinates.

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

Parameter schema for combined t-SNE calculation

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

ComboTsneParameters¶
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
spca_file_1	Path to first sPCA values file	NA	`InputFile`	str
spca_file_2	Path to second sPCA values file	NA	`InputFile`	str
output_file	Path to output file for t-SNE coordinates	NA	`OutputFile`	str
perplexity	Perplexity parameter for t-SNE	25.0	`Float`	float
n_iter	Number of iterations for t-SNE	20000	`Integer`	int

Functions

main(spca_file_1, spca_file_2, output_file, …)

Main runner function for script.

Classes

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

Parameter schema for combined t-SNE calculation