def get_argument_parser():
desc = 'Print information about GO-PCA run and output data.'
parser = arguments.get_argument_parser(desc=desc)
file_mv = arguments.file_mv
g = parser.add_argument_group('Input file (required)')
g.add_argument('-g',
'--gopca-file',
type=str,
required=True,
metavar=file_mv,
help='A GO-PCA run or result pickle.')
g.add_argument('-u',
'--print-user-config',
action='store_true',
help='Print user-provided GO-PCA config data of the run.')
g.add_argument('-s',
'--print-signatures',
action='store_true',
help='Print signatures of the GO-PCA result.')
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Extract GO-PCA signatures as a tab-delimited text file.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
return parser
def get_argument_parser():
desc = 'Extract the GO-PCA signatures matrix as a tab-delimited text file.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
arguments.add_signature_args(parser)
arguments.add_sample_args(parser)
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Converts GO-PCA result to MATLAB format.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
# arguments.add_reporting_args(parser)
parser.add_argument('--append-mat', action='store_true',
help='Automatically append .mat file extension.')
return parser
def get_argument_parser():
desc = 'Converts GO-PCA result to MATLAB format.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
# arguments.add_reporting_args(parser)
parser.add_argument('--append-mat',
action='store_true',
help='Automatically append .mat file extension.')
return parser
def get_argument_parser():
desc = 'Generate an interactive plot of the GO-PCA signature matrix.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
arguments.add_reporting_args(parser)
# arguments.add_sample_args(parser)
arguments.add_figure_args(parser)
arguments.add_heatmap_args(parser)
g = parser.add_argument_group('Plotting options')
g.add_argument(
'--no-plotly-js', action='store_true',
help='Do not include plotly javascript code in figure.')
return parser
def get_argument_parser():
desc = 'Filter redundant GO-PCA signatures.'
parser = arguments.get_argument_parser(desc=desc)
g = parser.add_argument_group('Filtering options')
arguments.add_io_args(parser)
float_mv = arguments.float_mv
g.add_argument(
'-r', '--corr-thresh', type=float, required=True, metavar=float_mv,
help=textwrap.dedent("""\
Correlation threshold for filtering signatures
(1.0 = off)."""))
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Combine the signatures from multiple GO-PCA analyses.'
parser = arguments.get_argument_parser(desc=desc)
file_mv = arguments.file_mv
g = parser.add_argument_group('Input and output files')
g.add_argument(
'-g', '--gopca-files', type=str, nargs='+', required=True,
metavar=file_mv,
help='List of GO-PCA output files with signatures to be merged.')
g.add_argument(
'-o', '--output-file', type=str, required=True, metavar=file_mv,
help='The output file.')
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Filter redundant GO-PCA signatures.'
parser = arguments.get_argument_parser(desc=desc)
g = parser.add_argument_group('Filtering options')
arguments.add_io_args(parser)
float_mv = arguments.float_mv
g.add_argument('-r',
'--corr-thresh',
type=float,
required=True,
metavar=float_mv,
help=textwrap.dedent("""\
Correlation threshold for filtering signatures
(1.0 = off)."""))
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Extract GO-PCA signatures as an Excel spreadsheet.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
return parser
def get_argument_parser():
desc = 'Extract GO-PCA signatures as a tab-delimited text file.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
arguments.add_reporting_args(parser)
return parser
def get_argument_parser():
desc = 'Extract GO-PCA signatures as an Excel spreadsheet.'
parser = arguments.get_argument_parser(desc=desc)
arguments.add_io_args(parser)
arguments.add_reporting_args(parser)
return parser
