def parse_arguments(args=None):
parser = argparse.ArgumentParser(
parents=[parserCommon.heatmapperMatrixArgs(),
parserCommon.heatmapperOutputArgs(mode='heatmap'),
parserCommon.heatmapperOptionalArgs(mode='heatmap')],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='This tool creates a heatmap for a '
'score associated to genomic regions. '
'The program requires a preprocessed matrix '
'generated by the tool computeMatrix.',
epilog='An example usage is: plotHeatmap -m <matrix file>',
add_help=False)
return parser
def parse_arguments(args=None):
parser = argparse.ArgumentParser(
parents=[parserCommon.heatmapperMatrixArgs(),
parserCommon.heatmapperOutputArgs(mode='heatmap'),
parserCommon.heatmapperOptionalArgs(mode='heatmap')],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='This tool creates a heatmap for '
'scores associated with genomic regions. '
'The program requires a matrix file '
'generated by the tool ``computeMatrix``.',
epilog='An example usage is: plotHeatmap -m <matrix file>',
add_help=False)
return parser
def parse_arguments(args=None):
parser = argparse.ArgumentParser(
parents=[parserCommon.heatmapperMatrixArgs(),
parserCommon.heatmapperOutputArgs(mode='profile'),
parserCommon.heatmapperOptionalArgs(mode='profile')],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='This tool creates a profile plot for '
'scores over sets of genomic regions. '
'Typically, these regions are genes, but '
'any other regions defined in BED '
' will work. A matrix generated '
'by computeMatrix is required.',
epilog='An example usage is: plotProfile -m <matrix file>',
add_help=False)
return parser
def parse_arguments(args=None):
parser = argparse.ArgumentParser(
parents=[parserCommon.heatmapperMatrixArgs(),
parserCommon.heatmapperOutputArgs(mode='profile'),
parserCommon.heatmapperOptionalArgs(mode='profile')],
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='This tool creates a profile plot for '
'scores over sets of genomic regions. '
'Typically, these regions are genes, but '
'any other regions defined in BED '
' will work. A matrix generated '
'by computeMatrix is required.',
epilog='An example usage is: plotProfile -m <matrix file>',
add_help=False)
return parser