.rst .pdf

repository open issue suggest edit

Contents

ALLCools.plot.genome_track._pygenometrack

Modified from pygenometracks LICENSE: https://github.com/deeptools/pyGenomeTracks/blob/master/LICENSE

Module Contents

FORMAT = [%(levelname)s:%(filename)s:%(lineno)s - %(funcName)20s()] %(message)s

log

DEFAULT_TRACK_HEIGHT = 0.5

DEFAULT_FIGURE_WIDTH = 40

DEFAULT_WIDTH_RATIOS = [0.01, 0.9, 0.1]

DEFAULT_MARGINS

class MultiDict

Bases: collections.OrderedDict

Class to allow identically named sections in configuration file by appending the section number for example: 1. section name

_unique = 0

__setitem__(self, key, val)

Set self[key] to value.

class PlotTracks(config, fig_width=DEFAULT_FIGURE_WIDTH, fig_height=None, fontsize=None, dpi=None, track_label_width=None, plot_regions=None, plot_width=None)

Bases: object

static get_available_tracks()

get_tracks_height(self, start_region=None, end_region=None)

The main purpose of the following loop is to get the height of each of the tracks because for the Hi-C the height is variable with respect to the range being plotted, the function is called when each plot is going to be printed.

Parameters

• start_region – start of the region to plot. Only used in case the plot is a Hi-C matrix

• end_region – end of the region to plot. Only used in case the plot is a Hi-C matrix

Returns:

plot(self, chrom, start, end, file_name=None, title=None, h_align_titles='left', decreasing_x_axis=False)

plot_vlines(self, axis_list, chrom_region, start_region, end_region)

Plots dotted lines from the top of the first plot to the bottom of the last plot at the specified positions.

Parameters

axis_list – list of plotted axis

:param chrom_region chromosome name :param start_region start position :param end_region end position

Returns

None

parse_tracks(self, tracks_file, plot_regions=None)

Parses a configuration file

Parameters

• tracks_file – file path containing the track configuration

• plot_regions – a list of tuple [(chrom1, start1, end1), (chrom2, start2, end2)] on which the data should be loaded here the vlines

Returns

array of dictionaries and vlines_file. One dictionary per track

close_files(self)

Close all opened files

static check_file_exists(track_dict, tracks_path, is_hic=False)

Checks if a file or list of files exists. If the file does not exist tries to check if the file may be relative to the track_file path, in such case the path is updated. :param track_dict: dictionary of track values. Should contain

a ‘file’ key containing the path of the file or files to be checked separated by space For example: file1 file2 file3

Parameters

• tracks_path – path of the tracks file

• is_hic –

Returns

None

static guess_filetype(track_dict, available_tracks)

Parameters

• track_dict – dictionary of track values with the ‘file’ key containing a string path of the file or files. Only the ending of the last file is used in case when there are more files

• available_tracks – list of available tracks

Returns

string file type detected

static cm2inch(*tupl)

static print_elapsed(start)

class SpacerTrack(properties_dict)

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 = []

TRACK_TYPE = spacer

DEFAULTS_PROPERTIES

NECESSARY_PROPERTIES = []

SYNONYMOUS_PROPERTIES

POSSIBLE_PROPERTIES

BOOLEAN_PROPERTIES = []

STRING_PROPERTIES = ['overlay_previous', 'title', 'file_type']

FLOAT_PROPERTIES

INTEGER_PROPERTIES

plot(self, ax, chrom_region, start_region, end_region)

plot_y_axis(self, ax, plot_ax)

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:

class XAxisTrack(*args, **kwargs)

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 = []

TRACK_TYPE = x_axis

NECESSARY_PROPERTIES = []

DEFAULTS_PROPERTIES

SYNONYMOUS_PROPERTIES

POSSIBLE_PROPERTIES

BOOLEAN_PROPERTIES = []

STRING_PROPERTIES = ['overlay_previous', 'title', 'where', 'file_type']

FLOAT_PROPERTIES

INTEGER_PROPERTIES

plot(self, ax, chrom_region, region_start, region_end)

plot_y_axis(self, ax, plot_ax)

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:

prepare_config(file_configs, add_spacer=True, spacer_height=0.5)

Prepare pyGenomeTracks config string.

Parameters

• file_configs – A list of file paths, or a list of file config dicts, containing file path and other config. See pyGenomeTracks documentation for possible parameters.

• add_spacer – Whether add spacer between tracks

• spacer_height – spacer height in cm

Returns

Return type

a single config string that can be read by PlotTracks

_prepare_track_config(file_config, track_type, track_class, add_spacer=True, spacer_height=0.5)

previous

ALLCools.plot.genome_track.HiCMatrixCoolTrack

next

ALLCools.plot.categorical_scatter