pybedtools.contrib.plotting.Track

class pybedtools.contrib.plotting.Track(features, chrom=None, ybase=0, yheight=1, visibility='dense', stranded=True, **kwargs)[source]
__init__(features, chrom=None, ybase=0, yheight=1, visibility='dense', stranded=True, **kwargs)[source]

Subclass of matplotlib’s PolyCollection that can be added to an Axes.

Parameters:

  • features – Can be an existing BedTool, or anything than can be used to create a BedTool (e.g., a filename or a generator of Interval objects)

  • ybase – y-coord of the bottom edge of the track (in data coordinates)

  • yheight – How high each feature will be, in data coordinates

  • visibility –

    Mimics the settings in the UCSC Genome Browser:

    • ”dense” is the default; overlapping features can be seen if you set alpha < 1.

    • ”squish” prevents adjacent features from overlapping. This keeps yheight for all features, so if you have a lot of features piling up, the track will be a lot higher on the y-axis than yheight.

  • stranded –

    If boolean and True, will draw arrrow-shaped features to indicate direction (where the point is 10% of the total gene length)

    If a dictionary, map strands to colors, e.g., {‘+’: ‘r’, ‘-’: ‘b’}.

  • kwargs – Additional keyword args are passed to matplotlib.collections.PolyCollection.

Notes:

After creating a track, use the ymax attribute to get the max y-value used in the track – useful if you’ve created a “squish” track but would like to stack another track on top, and need to calculate what the new Track’s ybase should be.

The returned PolyCollection will have the features attribute, which contains the BedTool it was created from – so you can write callback functions for event handling, e.g.:

def callback(event):
    '''
    prints the feature's line when clicked in the plot
    '''
    coll = event.artist
    for i in event.ind:
        print coll.features[i]

fig.canvas.mpl_connect('on_pick', callback)

>>> a = pybedtools.example_bedtool('a.bed')
>>> track = pybedtools.contrib.plotting.Track(a, alpha=0.5, picker=5)
>>> import matplotlib.pyplot as plt
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> ax.add_collection(track) 
<pybedtools.contrib.plotting.Track object at 0x...>
>>> limits = ax.axis('tight')

Methods

__init__(features[, chrom, ybase, yheight, ...])

Subclass of matplotlib's PolyCollection that can be added to an Axes.

add_callback(func)

Add a callback function that will be called whenever one of the .Artist's properties changes.

autoscale()

Autoscale the scalar limits on the norm instance using the current array

autoscale_None()

Autoscale the scalar limits on the norm instance using the current array, changing only limits that are None

changed()

Call this whenever the mappable is changed to notify all the callbackSM listeners to the 'changed' signal.

contains(mouseevent)

Test whether the mouse event occurred in the collection.

convert_xunits(x)

Convert x using the unit type of the xaxis.

convert_yunits(y)

Convert y using the unit type of the yaxis.

draw(renderer)

Draw the Artist (and its children) using the given renderer.

findobj([match, include_self])

Find artist objects.

format_cursor_data(data)

Return a string representation of data.

get_aa()

Alias for get_antialiased.

get_agg_filter()

Return filter function to be used for agg filter.

get_alpha()

Return the alpha value used for blending - not supported on all backends.

get_animated()

Return whether the artist is animated.

get_antialiased()

Get the antialiasing state for rendering.

get_antialiaseds()

Alias for get_antialiased.

get_array()

Return the array of values, that are mapped to colors.

get_capstyle()

Return the cap style for the collection (for all its elements).

get_children()

Return a list of the child .Artists of this .Artist.

get_clim()

Return the values (min, max) that are mapped to the colormap limits.

get_clip_box()

Return the clipbox.

get_clip_on()

Return whether the artist uses clipping.

get_clip_path()

Return the clip path.

get_cmap()

Return the .Colormap instance.

get_cursor_data(event)

Return the cursor data for a given event.

get_dashes()

Alias for get_linestyle.

get_datalim(transData)

get_ec()

Alias for get_edgecolor.

get_edgecolor()

get_edgecolors()

Alias for get_edgecolor.

get_facecolor()

get_facecolors()

Alias for get_facecolor.

get_fc()

Alias for get_facecolor.

get_figure()

Return the .Figure instance the artist belongs to.

get_fill()

Return whether face is colored.

get_gid()

Return the group id.

get_hatch()

Return the current hatching pattern.

get_in_layout()

Return boolean flag, True if artist is included in layout calculations.

get_joinstyle()

Return the join style for the collection (for all its elements).

get_label()

Return the label used for this artist in the legend.

get_linestyle()

get_linestyles()

Alias for get_linestyle.

get_linewidth()

get_linewidths()

Alias for get_linewidth.

get_ls()

Alias for get_linestyle.

get_lw()

Alias for get_linewidth.

get_mouseover()

Return whether this artist is queried for custom context information when the mouse cursor moves over it.

get_offset_transform()

Return the .Transform instance used by this artist offset.

get_offsets()

Return the offsets for the collection.

get_path_effects()

get_paths()

get_picker()

Return the picking behavior of the artist.

get_pickradius()

get_rasterized()

Return whether the artist is to be rasterized.

get_sizes()

Return the sizes ('areas') of the elements in the collection.

get_sketch_params()

Return the sketch parameters for the artist.

get_snap()

Return the snap setting.

get_tightbbox([renderer])

Like .Artist.get_window_extent, but includes any clipping.

get_transOffset()

Alias for get_offset_transform.

get_transform()

Return the .Transform instance used by this artist.

get_transformed_clip_path_and_affine()

Return the clip path with the non-affine part of its transformation applied, and the remaining affine part of its transformation.

get_transforms()

get_url()

Return the url.

get_urls()

Return a list of URLs, one for each element of the collection.

get_visible()

Return the visibility.

get_window_extent([renderer])

Get the artist's bounding box in display space.

get_xlims(ax)

Needs ax to convert to transData coords

get_zorder()

Return the artist's zorder.

have_units()

Return whether units are set on any axis.

is_transform_set()

Return whether the Artist has an explicitly set transform.

pchanged()

Call all of the registered callbacks.

pick(mouseevent)

Process a pick event.

pickable()

Return whether the artist is pickable.

properties()

Return a dictionary of all the properties of the artist.

remove()

Remove the artist from the figure if possible.

remove_callback(oid)

Remove a callback based on its observer id.

set(*[, agg_filter, alpha, animated, ...])

Set multiple properties at once.

set_aa(aa)

Alias for set_antialiased.

set_agg_filter(filter_func)

Set the agg filter.

set_alpha(alpha)

Set the alpha value used for blending - not supported on all backends.

set_animated(b)

Set whether the artist is intended to be used in an animation.

set_antialiased(aa)

Set the antialiasing state for rendering.

set_antialiaseds(aa)

Alias for set_antialiased.

set_array(A)

Set the value array from array-like A.

set_capstyle(cs)

Set the .CapStyle for the collection (for all its elements).

set_clim([vmin, vmax])

Set the norm limits for image scaling.

set_clip_box(clipbox)

Set the artist's clip .Bbox.

set_clip_on(b)

Set whether the artist uses clipping.

set_clip_path(path[, transform])

Set the artist's clip path.

set_cmap(cmap)

Set the colormap for luminance data.

set_color(c)

Set both the edgecolor and the facecolor.

set_dashes(ls)

Alias for set_linestyle.

set_ec(c)

Alias for set_edgecolor.

set_edgecolor(c)

Set the edgecolor(s) of the collection.

set_edgecolors(c)

Alias for set_edgecolor.

set_facecolor(c)

Set the facecolor(s) of the collection.

set_facecolors(c)

Alias for set_facecolor.

set_fc(c)

Alias for set_facecolor.

set_figure(fig)

Set the .Figure instance the artist belongs to.

set_gid(gid)

Set the (group) id for the artist.

set_hatch(hatch)

Set the hatching pattern

set_in_layout(in_layout)

Set if artist is to be included in layout calculations, E.g.

set_joinstyle(js)

Set the .JoinStyle for the collection (for all its elements).

set_label(s)

Set a label that will be displayed in the legend.

set_linestyle(ls)

Set the linestyle(s) for the collection.

set_linestyles(ls)

Alias for set_linestyle.

set_linewidth(lw)

Set the linewidth(s) for the collection.

set_linewidths(lw)

Alias for set_linewidth.

set_ls(ls)

Alias for set_linestyle.

set_lw(lw)

Alias for set_linewidth.

set_mouseover(mouseover)

Set whether this artist is queried for custom context information when the mouse cursor moves over it.

set_norm(norm)

Set the normalization instance.

set_offset_transform(offset_transform)

Set the artist offset transform.

set_offsets(offsets)

Set the offsets for the collection.

set_path_effects(path_effects)

Set the path effects.

set_paths(verts[, closed])

Set the vertices of the polygons.

set_picker(picker)

Define the picking behavior of the artist.

set_pickradius(pickradius)

Set the pick radius used for containment tests.

set_rasterized(rasterized)

Force rasterized (bitmap) drawing for vector graphics output.

set_sizes(sizes[, dpi])

Set the sizes of each member of the collection.

set_sketch_params([scale, length, randomness])

Set the sketch parameters.

set_snap(snap)

Set the snapping behavior.

set_transOffset(offset_transform)

Alias for set_offset_transform.

set_transform(t)

Set the artist transform.

set_url(url)

Set the url for the artist.

set_urls(urls)

Parameters:

set_verts(verts[, closed])

Set the vertices of the polygons.

set_verts_and_codes(verts, codes)

Initialize vertices with path codes.

set_visible(b)

Set the artist's visibility.

set_zorder(level)

Set the zorder for the artist.

span_where(x, ymin, ymax, where, **kwargs)

[Deprecated] Return a .BrokenBarHCollection that plots horizontal bars from over the regions in x where where is True.

to_rgba(x[, alpha, bytes, norm])

Return a normalized RGBA array corresponding to x.

update(props)

Update this artist's properties from the dict props.

update_from(other)

Copy properties from other to self.

update_scalarmappable()

Update colors from the scalar mappable array, if any.

Attributes

axes

The ~.axes.Axes instance the artist resides in, or None.

midpoint

mouseover

Return whether this artist is queried for custom context information when the mouse cursor moves over it.

norm

stale

Whether the artist is 'stale' and needs to be re-drawn for the output to match the internal state of the artist.

sticky_edges

x and y sticky edge lists for autoscaling.

zorder

colorbar

The last colorbar associated with this ScalarMappable.