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ALLCools.plot.genome_track

ALLCools.plot.genome_track

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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)[source]

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)
prepare_config(file_configs, add_spacer=True, spacer_height=0.5)[source]

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

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