def __init__(self,
data,
window_sizes=None,
regions=None,
title='',
midpoint=None,
colormap='coolwarm_r',
vmax=None,
current_window_size=0,
log_y=True):
if regions is None:
regions = []
for i in range(data.shape[1]):
regions.append(GenomicRegion(chromosome='', start=i, end=i))
self.regions = regions
BasePlotter1D.__init__(self, title=title)
self.da = data
if window_sizes is None:
window_sizes = []
try:
l = len(data)
except TypeError:
l = data.shape[0]
for i in range(l):
window_sizes.append(i)
self.window_sizes = window_sizes
self.colormap = colormap
self.midpoint = midpoint
self.mesh = None
self.vmax = vmax
self.window_size_line = None
self.current_window_size = current_window_size
self.log_y = log_y
def plot(self, region=None, ax=None, **kwargs):
if isinstance(region, string_types):
region = GenomicRegion.from_string(region)
if ax:
self.ax = ax
# set genome tick formatter
self.ax.xaxis.set_major_formatter(GenomeCoordFormatter(region))
self.ax.xaxis.set_major_locator(GenomeCoordLocator(nbins=5))
self.ax.xaxis.set_minor_locator(MinorGenomeCoordLocator(n=5))
self.ax.set_title(self.title)
self._plot(region, **kwargs)
self.ax.set_xlim(region.start, region.end)
return self.fig, self.ax
def plot(self, region=None, ax=None, **kwargs):
if isinstance(region, string_types):
region = GenomicRegion.from_string(region)
if ax:
self.ax = ax
# set genome tick formatter
self.ax.xaxis.set_major_formatter(GenomeCoordFormatter(region))
self.ax.xaxis.set_major_locator(GenomeCoordLocator(nbins=5))
self.ax.xaxis.set_minor_locator(MinorGenomeCoordLocator(n=5))
self.ax.set_title(self.title)
self._plot(region, **kwargs)
self.ax.set_xlim(region.start, region.end)
return self.fig, self.ax
def __init__(self,
data,
regions=None,
title='',
init_row=0,
is_symmetric=False):
BasePlotter1D.__init__(self, title=title)
if regions is None:
regions = []
for i in range(len(data)):
regions.append(GenomicRegion(chromosome='', start=i, end=i))
self.init_row = init_row
self.data = data
self.sr = None
self.da_sub = None
self.regions = regions
self.current_region = None
self.line = None
self.current_ix = init_row
self.current_cutoff = None
self.cutoff_line = None
self.cutoff_line_mirror = None
self.is_symmetric = is_symmetric
def __init__(self,
hic_matrix,
regions=None,
colormap='RdBu',
norm="log",
vmin=None,
vmax=None,
show_colorbar=True,
blend_masked=False):
if regions is None:
for i in range(hic_matrix.shape[0]):
regions.append(GenomicRegion(chromosome='', start=i, end=i))
self.regions = regions
self.hic_matrix = hic_matrix
self.colormap = copy.copy(mpl.cm.get_cmap(colormap))
if blend_masked:
self.colormap.set_bad(self.colormap(0))
self._vmin = vmin
self._vmax = vmax
self.norm = prepare_normalization(norm=norm, vmin=vmin, vmax=vmax)
self.colorbar = None
self.slider = None
self.show_colorbar = show_colorbar
def __init__(self,
hic_matrix,
regions=None,
data=None,
window_sizes=None,
norm='lin',
max_dist=3000000,
max_percentile=99.99,
algorithm='insulation',
matrix_colormap=None,
data_colormap=None,
log_data=True):
self.hic_matrix = hic_matrix
if regions is None:
regions = []
for i in range(hic_matrix.shape[0]):
regions.append(GenomicRegion(chromosome='', start=i, end=i))
self.regions = regions
self.norm = norm
self.fig = None
self.max_dist = max_dist
self.algorithm = algorithm
self.svmax = None
self.min_value = np.nanmin(self.hic_matrix[np.nonzero(
self.hic_matrix)])
self.min_value_data = None
self.hic_plot = None
self.tad_plot = None
self.data_plot = None
self.line_plot = None
self.sdata = None
self.data_ax = None
self.line_ax = None
self.da = None
self.ws = None
self.current_window_size = None
self.window_size_text = None
self.tad_cutoff_text = None
self.max_percentile = max_percentile
self.tad_regions = None
self.current_da_ix = None
self.button_save_tads = None
self.button_save_vector = None
self.button_save_matrix = None
self.log_data = log_data
if algorithm == 'insulation':
self.tad_algorithm = insulation_index
self.tad_calling_algorithm = call_tads_insulation_index
self.is_symmetric = False
if matrix_colormap is None:
self.matrix_colormap = LinearSegmentedColormap.from_list(
'myreds', ['white', 'red'])
if data_colormap is None:
self.data_plot_color = 'plasma'
elif algorithm == 'ninsulation':
self.tad_algorithm = normalised_insulation_index
self.tad_calling_algorithm = call_tads_insulation_index
self.is_symmetric = True
if matrix_colormap is None:
self.matrix_colormap = LinearSegmentedColormap.from_list(
'myreds', ['white', 'red'])
if data_colormap is None:
self.data_plot_color = LinearSegmentedColormap.from_list(
'myreds', ['blue', 'white', 'red'])
elif algorithm == 'directionality':
self.tad_algorithm = directionality_index
self.tad_calling_algorithm = call_tads_directionality_index
self.is_symmetric = True
if matrix_colormap is None:
self.matrix_colormap = LinearSegmentedColormap.from_list(
'myreds', ['white', 'red'])
if data_colormap is None:
self.data_plot_color = LinearSegmentedColormap.from_list(
'myreds', ['blue', 'white', 'red'])
if data is None:
self.da, self.ws = data_array(hic_matrix=self.hic_matrix,
regions=self.regions,
tad_method=self.tad_algorithm,
window_sizes=window_sizes)
else:
self.da = data
if window_sizes is None:
raise ValueError(
"window_sizes parameter cannot be None when providing data!"
)
self.ws = window_sizes