lib5c.plotters.extendable.ruler_extendable_heatmap module

Module for the RulerExtendableHeatmap class, which adds ruler track plotting functionality for the extendable heatmap system.

class lib5c.plotters.extendable.ruler_extendable_heatmap.RulerExtendableHeatmap(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 ruler track plotting functionality.

add_ruler(loc='bottom', size='5%', pad=0.0, new_ax_name='ruler', axis_limits=(1, 0), ruler_tick_height=0.3, ruler_text_baseline=0.5, no_ticks=False, fontsize=7, no_tick_precision=2)[source]

Adds one ruler track along either the x- or y-axis of the heatmap.

Parameters
  • loc ({'top', 'bottom', 'left', 'right'}) – Which side of the heatmap to add the new ruler track to.

  • size (str) – The size of the new axis as a percentage of the main heatmap width. Should be passed as a string ending in ‘%’.

  • pad (float) – The padding to use between the existing parts of the figure and the newly added axis.

  • new_ax_name (str) – The name for the newly created axis.

  • axis_limits (tuple of float) – Axis limits for the non-genomic axis of the ruler track.

  • ruler_tick_height (float) – The height of the ruler ticks.

  • ruler_text_baseline (float) – Controls how far away from the top of the new axis the text elements (chromosome name and region size) will be drawn.

  • no_ticks (bool) – Pass True to skip plotting ruler ticks, and instead write the start and end coordinate of the plotted region in units of megabase pairs.

  • fontsize (float) – The font size to use for adding labels to the ruler axis.

  • no_tick_precision (int) – When no_ticks is True, round the start and end coordinates of the plotted region to this many digits after the decimal.

Returns

The newly added ruler track axis.

Return type

pyplot axis

add_rulers(size='5%', pad=0.0, axis_limits=(1, 0), ruler_tick_height=0.3, ruler_text_baseline=0.5, no_ticks=False, fontsize=7, no_tick_precision=2)[source]

Adds a ruler track to both the bottom and left side of the heatmap by calling add_ruler() twice.

Parameters
  • size (str) – The size of the new axis as a percentage of the main heatmap width. Should be passed as a string ending in ‘%’.

  • pad (float) – The padding to use between the existing parts of the figure and the newly added axis.

  • axis_limits (tuple of float) – Axis limits for the non-genomic axis of the ruler track.

  • ruler_tick_height (float) – The height of the ruler ticks.

  • ruler_text_baseline (float) – Controls how far away from the top of the new axis the text elements (chromosome name and region size) will be drawn.

  • no_ticks (bool) – Pass True to skip plotting ruler ticks, and instead write the start and end coordinate of the plotted region in units of megabase pairs.

  • fontsize (float) – The font size to use for adding labels to the ruler axis.

  • no_tick_precision (int) – When no_ticks is True, round the start and end coordinates of the plotted region to this many digits after the decimal.

Returns

The newly added gene ruler axes.

Return type

list of pyplot axes