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.

add_checker(checker)

Add an entry to a dictionary of boolean flags that are set to True when the mappable is changed.

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

check_update(checker)

If mappable has changed since the last check, return True; else return False

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 using the given renderer.

findobj([match, include_self])

Find artist objects.

format_cursor_data(data)

Return a string representation of data.

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 the animated state.

get_array()

Return the array

get_capstyle()

get_children()

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

get_clim()

return the min, max of the color limits for image scaling

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

get_contains()

Return the custom contains function of the artist if set, or None.

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 fill is set

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()

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_offset_position()

Returns how offsets are applied for the collection.

get_offset_transform()

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()

Returns the sizes of the elements in the collection.

get_sketch_params()

Returns the sketch parameters for the artist.

get_snap()

Returns the snap setting.

get_tightbbox(renderer)

Like Artist.get_window_extent, but includes any clipping.

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()

get_visible()

Return the visibility.

get_window_extent(renderer)

Get the axes 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 True if 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(**kwargs)

A property batch setter.

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 the artist’s animation state.

set_antialiased(aa)

Set the antialiasing state for rendering.

set_antialiaseds(aa)

Alias for set_antialiased.

set_array(A)

Set the image array from numpy array 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_contains(picker)

Define a custom contains test for the artist.

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_norm(norm)

Set the normalization instance.

set_offset_position(offset_position)

Set how offsets are applied.

set_offsets(offsets)

Set the offsets for the collection.

set_path_effects(path_effects)

Set the path effects.

set_paths(verts[, closed])

This allows one to delay initialization of the vertices.

set_picker(picker)

Define the picking behavior of the artist.

set_pickradius(pr)

Set the pick radius used for containment tests.

set_rasterized(rasterized)

Force rasterized (bitmap) drawing in vector backend output.

set_sizes(sizes[, dpi])

Set the sizes of each member of the collection.

set_sketch_params([scale, length, randomness])

Sets the sketch parameters.

set_snap(snap)

Set the snapping behavior.

set_transform(t)

Set the artist transform.

set_url(url)

Set the url for the artist.

set_urls(urls)

Parameters

set_verts(verts[, closed])

This allows one to delay initialization of the vertices.

set_verts_and_codes(verts, codes)

This allows one to initialize vertices with path codes.

set_visible(b)

Set the artist’s visibility.

set_zorder(level)

Set the zorder for the artist.

to_rgba(x[, alpha, bytes, norm])

Return a normalized rgba array corresponding to x.

update(props)

Update this artist’s properties from the dictionary props.

update_from(other)

copy properties from other to self

update_scalarmappable()

Update colors from the scalar mappable array, if it is not None.

Attributes

aname

axes

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

midpoint

mouseover

If this property is set to True, the artist will be queried for custom context information when the mouse cursor moves over it.

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