def __init__(self, *args, **kwargs):
TrackPlot.__init__(self, *args, **kwargs)
if 'color' not in self.properties:
self.properties['color'] = PlotBedGraph.DEFAULT_COLOR
self.interval_tree, ymin, ymax = file_to_intervaltree(self.properties['file'])
if 'max_value' not in self.properties or self.properties['max_value'] == 'auto':
self.properties['max_value'] = ymax
if 'min_value' not in self.properties or self.properties['min_value'] == 'auto':
self.properties['min_value'] = ymin
def __init__(self, file_, **kwargs):
properties_dict = {
"file": file_,
"color": "#1e1e1e",
"alpha": 0.8,
"line_style": "dashed",
"line_width": 1,
}
properties_dict.update(kwargs)
super().__init__(properties_dict)
self.vlines_intval_tree, _, _ = file_to_intervaltree(self.properties['file'])
def __init__(self, file_, **kwargs):
properties_dict = {
'file': file_,
'color_scheme': Ideogram.DEFAULT_COLOR_SCHEME,
'show_name': True,
'font_size': Ideogram.DEFAULT_FONT_SIZE,
'border_color': '#000000',
'border_width': Ideogram.DEFAULT_BORDER_WIDTH,
'height': Ideogram.DEFAULT_HEIGHT,
'title': '',
}
properties_dict.update(kwargs)
super().__init__(properties_dict)
self.file = self.properties['file']
self.interval_tree, _, _ = file_to_intervaltree(self.file)
def __init__(self, *args, **kwargs):
TrackPlot.__init__(self, *args, **kwargs)
if 'height' not in self.properties:
self.properties['height'] = PlotIdeogram.DEFAULT_HEIGHT
if 'show_band_name' not in self.properties:
self.properties['show_band_name'] = 'yes'
if 'font_size' not in self.properties:
self.properties['font_size'] = PlotIdeogram.DEFAULT_FONT_SIZE
if 'color_scheme' not in self.properties:
self.properties['color_scheme'] = PlotIdeogram.DEFAULT_COLOR_SCHEME
if 'border_color' not in self.properties:
self.properties['border_color'] = PlotIdeogram.DEFAULT_BORDER_COLOR
if 'border_width' not in self.properties:
self.properties['border_width'] = PlotIdeogram.DEFAULT_BORDER_WIDTH
self.file = self.properties['file']
self.interval_tree, _, _ = file_to_intervaltree(self.file)
def __init__(self, *args, **kwargs):
CoveragePlot.__init__(self, *args, **kwargs)
if 'line_width' not in self.properties:
self.properties['line_width'] = PlotVlines.DEFAULT_LINE_WIDTH
if 'line_style' not in self.properties:
self.properties['line_style'] = PlotVlines.DEFAULT_LINE_STYLE
if 'color' not in self.properties:
self.properties['color'] = PlotVlines.DEFAULT_COLOR
if 'alpha' not in self.properties:
self.properties['alpha'] = PlotVlines.DEFAULT_ALPHA
if 'file' in self.properties:
# plot vlines from file
self.vlines_intval_tree, _, _ = file_to_intervaltree(
self.properties['file'])
else:
self.vlines_intval_tree = self.__intervaltree_from_list(
self.properties['vlines_list'])