lib5c.plotters.extendable.rectangle_extendable_heatmap module

Module for the RectangleExtendableHeatmap class, which adds rectangle outlining functionality to the extendable heatmap system.

class lib5c.plotters.extendable.rectangle_extendable_heatmap.RectangleExtendableHeatmap(array, grange_x, grange_y=None, colorscale=None, colormap='obs', norm=None)[source]

Bases: lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap

ExtendableHeatmap mixin class providing rectangle outlining functionality.

Unlike cluster outlining, which outlines specific pixels of the heatmap, or domain outlining, which outlines the upper or lower triangles of diagonal- aligned squares corresponding to domains, rectangle outlining simply draws a rectangle on the heatmap whose sides are described by genomic ranges.

This can be used to outline cluster bounding boxes.

add_rectangle(coords, color='#00FF00', weight='100x', transpose=True)[source]

Draw some rectangles (specified in genomic coordinates) on the heatmap.

Parameters

  • coords (tuple of dict or str) –

    Genomic coordinates for the rectangle to be plotted. Can be a tuple:

    ({'chrom': str, 'start': int, 'end': int},
 {'chrom': str, 'start': int, 'end': int})

    where the first dict specifies the genomic coordinates of one side of the rectangle, and the second dict specifies the genomic coordinates of the other side. Can also be a string of the form chrom:start-end_chrom:start-end, where the _ separates genomic ranges which specify the coordinates of the two sides of the rectangle.

  • color (valid matplotlib color) – The edge color to draw the rectangle with.

  • weight (int or str) – The line width to use to draw the rectangle. Pass a string of the form '100x' to specify the line width as a multiple of the inverse of the size of this heatmap’s array.

  • transpose (bool) – Pass True to interpret the first feature in coords as the side of the rectangle parallel to the y-axis. Pass False to interpret it as the side parallel to the x-axis.

add_rectangles(coords_list, color='#00FF00', weight='100x', transpose=True)[source]

Draw some rectangles (specified in genomic coordinates) on the heatmap.

Parameters

  • coords_list (list of tuple of dict or list of str) –

    List of sets genomic coordinates (one set for each rectangle) to be plotted. The list can contain tuples:

    ({'chrom': str, 'start': int, 'end': int},
 {'chrom': str, 'start': int, 'end': int})

    where the first dict specifies the genomic coordinates of one side of the rectangle, and the second dict specifies the genomic coordinates of the other side. The list can also contain strings of the form chrom:start-end_chrom:start-end, where the _ separates genomic ranges which specify the coordinates of the two sides of the rectangle.

  • color (valid matplotlib color) – The edge color to draw the rectangles with.

  • weight (int or str) – The line width to use to draw the rectangles. Pass a string of the form '100x' to specify the line width as a multiple of the inverse of the size of this heatmap’s array.

  • transpose (bool) – Pass True to interpret the first feature in each tuple or string as the side of the rectangle parallel to the y-axis. Pass False to interpret it as the side parallel to the x-axis.