In addition to matrix-based plots, FAN-C provides a number of plots to plot genomic tracks alongside Hi-C data (although they can certainly also be used independently). The main plots in this category are
- :class:`~fanc.plotting.plotter.LinePlot`, which plots (ideally continuous) scores associated with genomic regions as a line plot.
- :class:`~fanc.plotting.plotter.BarPlot`, which plots genomic region scores as bars
- :class:`~fanc.plotting.plotter.GenomicVectorArrayPlot`, which plots multiple scores associated with the same regions, such as insulation scores at different window sizes, as a heatmap
- :class:`~fanc.plotting.plotter.FeatureLayerPlot`, which plots the location of features as blocks, grouped by user-specified attributes, such as the location TAD boundaries in different matrices
- :class:`~fanc.plotting.plotter.GenePlot`, which, as the name suggests, can plot gene and transcript annotations, including exon-intron structures.
:class:`~fanc.plotting.plotter.LinePlot` accepts a :class:`~genomic_regions.RegionBased` object as input. These can be created very easily from any compatible genomic regions format, including BED, GFF/GTF, BigWig, Tabix, and more. So let's load some BED files:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot load bed
:end-before: end snippet fancplot load bed
We can then use that directly as input:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line fill
:end-before: end snippet fancplot line fill
By default, FAN-C fills the area between the X axis and the curve. We can disable that using
fill=False:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line nofill
:end-before: end snippet fancplot line nofill
Instead of the step-wise style of the line, we can only connect points at each midpoint of the genomic regions:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line mid
:end-before: end snippet fancplot line mid
We can change the color of the line with colors. Other plot aspects affecting the line drawing,
passed to the internal matplotlib ax.plot function, can be controlled through the plot_kwargs
dictionary, as shown here for transparency:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line col
:end-before: end snippet fancplot line col
Finally, we can control the y axis limits with ylim (or you can use a custom axis.
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line ylim
:end-before: end snippet fancplot line ylim
It is also possible to add multiple score tracks to the same :class:`~fanc.plotting.plotter.LinePlot`:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot line multi
:end-before: end snippet fancplot line multi
The :class:`~fanc.plotting.plotter.BarPlot` works in virtually the same way as the :class:`~fanc.plotting.plotter.LinePlot`:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot bar basic
:end-before: end snippet fancplot bar basic
In addition, it also works very well for non-continuous data, such as shown here for domain boundaries in a larger interval:
.. literalinclude:: code/region_plot_examples.py
:language: python
:start-after: start snippet fancplot bar boundaries
:end-before: end snippet fancplot bar boundaries
