Error creating PyClone plots

[Rui Resende]

Hello, I am running PyClone run_analysis_pipeline but it is throwing an error when creating the plots. It created all of the output except the locus specific plots. The error is the following:

 

Traceback (most recent call last):

  File "/opt/conda/bin/PyClone", line 11, in <module>

    load_entry_point('PyClone==0.13.1', 'console_scripts', 'PyClone')()

  File "/opt/conda/lib/python2.7/site-packages/pyclone/cli.py", line 78, in main

    args.func(args)

  File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 109, in run_analysis_pipeline

    thin=args.thin

  File "/opt/conda/lib/python2.7/site-packages/pyclone/run.py", line 479, in _loci_plot

    **kwargs

  File "/opt/conda/lib/python2.7/site-packages/pyclone/post_process/plot/loci.py", line 105, in density_plot

    grid.tight_layout(fig, h_pad=3)

  File "/opt/conda/lib/python2.7/site-packages/matplotlib/gridspec.py", line 318, in tight_layout

    renderer = tight_layout.get_renderer(figure)

  File "/opt/conda/lib/python2.7/site-packages/matplotlib/tight_layout.py", line 204, in get_renderer

    renderer = canvas.get_renderer()

  File "/opt/conda/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 450, in get_renderer

    self.renderer = RendererAgg(w, h, self.figure.dpi)

  File "/opt/conda/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 97, in __init__

    self._renderer = _RendererAgg(int(width), int(height), dpi)

ValueError: Image size of 800x148400 pixels is too large. It must be less than 2^16 in each direction.

Does anyone know the problem?

Thank you for your attention!

[Andrew]

Hi Rui,

If you using a lot mutations, the default plotting in PyClone will break. The best solution is to run the steps in the pipeline manually, and skip the plots by loci. You can use the `build_table` command to get tsv files that you can plot manually.

Best wishes,

Andy