`circhic`.CircHiCFigure¶

class circhic.CircHiCFigure(lengths, origin=1, chromosome_type='circular', figure=None)¶

A circular HiC figure

Parameters

lengths : ndarray: array of chromosome length.
origininteger, optional, default: 1: position of the origin. The origin is set to the North of the plot
chromosome_type{“circular”, “linear”}, optional, default: “circular”: whether to plot a circular or a linear chromosome.
figure : matplotlib.figure.Figure, optional, default: None: A Matplotlib figure. If not provided, will create it.

Notes

See FIXME

Methods

`plot_bands`(begin, end[, colors, ...])	Plot bands
`plot_bars`(data[, color, inner_radius, ...])	Plot a bar chart
`plot_hic`(counts[, inner_gdis, outer_gdis, ...])	Plot a heatmap of the HiC contact count matrix on a circular strip.
`plot_lines`(data[, color, linestyle, ...])	Plot a line chart
`plot_raxis`()	Plot the r-axis, corresponding to the genomic distance
`set_colorbar`(mappable[, orientation, ...])	Set a colorbar on the plot
`set_genomic_ticklabels`([outer_radius, ...])	Set the circular tick labels

__init__(lengths, origin=1, chromosome_type='circular', figure=None)¶

plot_bands(begin, end, colors=None, inner_radius=0, outer_radius=1)¶

Plot bands

Parameters

beginndarray (l, ): List of the all the beginnings of each band.
endndarray (l, ): List of all the ends of each band.
colorsndarray (l, ): List of colors. Should be the same size as begin and end

Returns

(artists, ax)

plot_bars(data, color=None, inner_radius=0, outer_radius=1, zorder=None)¶

Plot a bar chart

Parameters

datandarray (n, )

colora compatible matplotlib color, optional, default: None

The line color. Possible values:

A single color format string (e.g. “#000000”, “black”, “0”).
A float between 0 and 1

Defaults to None.

linestylea compatible Matplotlib linestyle, optional, default: None

inner_radius : float (0, 1), optional, default: 0

The inner radius of the plot, assuming the maximum outer radius possible is 1. Should be smaller than outer_radius.

outer_radius : float (0, 1), optional, default: 1

The outer radius of the plot, assuming the maximum outer radius possible is 1. Should be larger than inner_radius.

zorderfloat

Returns

(artists, ax)

plot_hic(counts, inner_gdis=None, outer_gdis=None, inner_radius=0, outer_radius=1, resolution=1, cmap='viridis', mode='reflect', vmin=None, vmax=None, alpha=1, border_thickness=0.02, ax=None, granularity=0.5)¶

Plot a heatmap of the HiC contact count matrix on a circular strip.

Parameters

counts : ndarray (n, n)

The contact count matrix of shape (n, n) where n = lengths.sum() / resolution

inner_gdisinteger, optional, default: None

Plot up to inner_gdis of the diagonal of the contact count matrix (in genomic distance). Corresponds to the lower-diagonal on a typical square HiC contact count matrix.

outer_gdisinteger, optional, default: None

Plot up to outer_gdis of the diagonal of the contact count matrix (in genomic distance). Corresponds to the upper-diagonal part of the contact count matrix on a typical square contact count map.

inner_radius : float, optional, default: 0

Radius of the inner strip, considering that the maximum outer radius is 1. Should be smaller than outer_radius. Note that inner_radius will be ignored if ax is provided.

outer_radiusfloat, optional, default: 1

Radius of the outer strip, considering that the maximum possible outer radius is 1. Should be larger than inner_radius.

resolution : integer, optional, default: None

Resolution of the HiC contact count map. By default, the function will estimate the resolution given the lengths of the chromosome and the shape of the contact count matrix.

cmapstring, optional, default

A Matplotlib colormap.

mode{“reflect”, “distant”}, optional, default: “reflect”

if “reflect”, the contact count matrix will be plotted from inner_gdis to 0, then 0 to outer_gdis.
if “distant”, the contact count matrix will be plotted from inner_gdis to outer_gdis: this option is useful to visualize contact counts far away from the diagonal.

vmin, vmaxfloat, optional, default: None

vmin and vmax define the data range that the colormap covers. By default, the colormap covers the complete value range of the supplied data.

axmatplotlib.axes.Axes object, optional, default: None

Matplotlib Axes object. By default, will create one. Note that outer_radius and inner_radius will be ignored if ax is provided.

Returns

(im, ax) type of artist and axes

plot_lines(data, color=None, linestyle=None, inner_radius=0, outer_radius=1, zorder=None)¶

Plot a line chart

Parameters

datandarray (n, )

colora compatible matplotlib color, optional, default: None

The line color. Possible values:

A single color format string (e.g. “#000000”, “black”, “0”).
A float between 0 and 1

Defaults to None.

linestylea compatible Matplotlib linestyle, optional, default: None

inner_radius : float (0, 1), optional, default: 0

The inner radius of the plot, assuming the maximum outer radius possible is 1. Should be smaller than outer_radius.

outer_radius : float (0, 1), optional, default: 1

The outer radius of the plot, assuming the maximum outer radius possible is 1. Should be larger than inner_radius.

zorderfloat

Returns

(lines, ax)

plot_raxis()¶: Plot the r-axis, corresponding to the genomic distance

set_colorbar(mappable, orientation='vertical', tick_formatter=None)¶

Set a colorbar on the plot

Parameters

mappable : matplotlib.cm.ScalarMappable: The matplotlib.cm.ScalarMappable (i.e., Image, ContourSet, etc.) described by this colorbar.
orientation{“vertical”, “horizontal”}, default: “vertical”: Whether to plot a vertical or horizontal colorbar.

set_genomic_ticklabels(outer_radius=1, ticklabels=None, tickpositions=None, fontdict=None, ax=None)¶