ALLCools.plot.genome_track.HiCMatrixCoolTrack

Module Contents

DEFAULT_MATRIX_COLORMAP = RdYlBu_r[source]
log[source]
class HiCMatrixCoolTrack(*args, **kwargs)[source]

Bases: pygenometracks.tracks.GenomeTrack.GenomeTrack

The GenomeTrack object is a holder for all tracks that are to be plotted. For example, to plot a bedgraph file a new class that extends GenomeTrack should be created.

It is expected that all GenomeTrack objects have a plot method.

SUPPORTED_ENDINGS = ['.cool', '.mcool'][source]
TRACK_TYPE = cooler[source]
OPTIONS_TXT[source]
DEFAULTS_PROPERTIES[source]
NECESSARY_PROPERTIES = ['file'][source]
SYNONYMOUS_PROPERTIES[source]
POSSIBLE_PROPERTIES[source]
BOOLEAN_PROPERTIES = ['show_masked_bins', 'rasterize'][source]
STRING_PROPERTIES = ['file', 'file_type', 'overlay_previous', 'orientation', 'transform', 'title', 'colormap'][source]
FLOAT_PROPERTIES[source]
INTEGER_PROPERTIES[source]
set_properties_defaults(self)[source]
plot(self, ax, chrom_region, region_start, region_end)[source]
plot_y_axis(self, cbar_ax, plot_ax)[source]

Plot the scale of the y axis with respect to the plot_axis :param ax: axis to use to plot the scale :param plot_axis: the reference axis to get the max and min. :param transform: what was the transformation of the data :param log_pseudocount: :param y_axis: ‘tranformed’ or ‘original’ :param only_at_ticks: False: only min_max are diplayed

True: only ticks values are displayed

Returns:

pcolormesh_45deg(self, ax, matrix_c, start_pos_vector)[source]

Turns the matrix 45 degrees and adjusts the bins to match the actual start end positions.