scvis

#!/usr/bin/env python

# scvis
# Author : Jiarui Ding <jiarui.ding@gmail.com>

import argparse

from scvis.run import train, map

parser = argparse.ArgumentParser(prog='scvis')

parser.add_argument('--version', action='version', version='0.1.0')


# The common arguments
analysis_parser = argparse.ArgumentParser(add_help=False)


analysis_parser.add_argument('--data_matrix_file',
                             required=True,
                             help='''The high-dimensional data matrix''')

analysis_parser.add_argument('--config_file',
                             default=None,
                             help='''Path to a yaml format configuration file''')

analysis_parser.add_argument('--out_dir',
                             default="output",
                             help='''Path for output files''')

analysis_parser.add_argument('--data_label_file',
                             default=None,
                             help='''Just used for colouring scatter plots''')


# Learning a parametric mapping
subparsers = parser.add_subparsers()

train_parser = subparsers.add_parser('train',
                                     parents=[analysis_parser],
                                     help='''Learning a parametric mapping for high-dimensional single cell data''')

train_parser.add_argument('--pretrained_model_file',
                          default=None,
                          help='''A pretrained scvis model, continue to train this model''')

train_parser.add_argument('--normalize',
                          type=float,
                          required=False,
                          help='''The data will be divided by this number if provided (default: the maximum value).''')

train_parser.add_argument('--verbose',
                          required=False,
                          action='store_true',
                          help='''Print running information''')

train_parser.add_argument('--verbose_interval',
                          default=50,
                          required=False,
                          type=int,
                          help='''Print running information after running # of mini-batches''')

train_parser.add_argument('--show_plot',
                          required=False,
                          action='store_true',
                          help='''Plot intermediate embedding when this parameter is set''')

train_parser.set_defaults(func=train)


# Mapping new data
test_parser = subparsers.add_parser('map',
                                    parents=[analysis_parser],
                                    help='''Mapping high-dimensional single cell data to a low-dimensional space
                                            given a pretrained mapping''')

test_parser.add_argument('--pretrained_model_file',
                         required=True,
                         help='''A pretrained scvis model used to map new data''')

test_parser.add_argument('--normalize',
                         required=False,
                         type=float,
                         help='''Data will be divided by this number if provided (default: from the trained model)''')

test_parser.set_defaults(func=map)


# The arguments
args = parser.parse_args()

args.func(args)