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Subclonal Hierarchy Inference from Somatic Mutations

License: Other

Python 98.71% Dockerfile 1.29%

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al3n70rn alenzhao ctokheim xtmgah benzene1987 arshah18 nihilee thz34

schism's Issues

nan value in Hypothesis Testing

I'm getting a nan value on the Hypothesis testing while running the Step-Through mode. It seems that if the s.d. of some samples were 0 in the .cellularity file after using the prepare_for_hypothesist_test command. Once I added a small s.d. the issue resolved. Not sure if that's the appropriate course of action though.

Is this a bug?

Tree construction failed at last step

Hi Niknafs:

I try to use SCHISM to construct tree using data generated by Pyclone.

It works fine for the first 5 steps in 'step through' mode but failed at the last step.
The error message is:
'Traceback (most recent call last):
File "/anaconda2/bin/runSchism", line 155, in
main()
File "/anaconda2/bin/runSchism", line 152, in main
args.func(args)
File "/anaconda2/lib/python2.7/site-packages/SCHISM/GA.py", line 136, in generate_consensus_tree
plot_consensus_tree(args)
File "/anaconda2/lib/python2.7/site-packages/SCHISM/visualize.py", line 325, in plot_consensus_tree
root = list(set(vertices) - set(zip(*edges)[1]))[0]
IndexError: list index out of range'

I can't see what is going wrong, I also got my "E2.GA.consensusTree", which looks like:
c

Required vs optional CLI arguments

Is the config file a required argument? Might be nice to add required=True so that argparse catches this, or if there is default then put a default=XXX in the add_argument method. Not sure if other parameters might need this.

the download link of Cairo and PyCairo package

hi，
I want to download the Cairo and PyCairo package, but i canot open the link:https://gist.github.com/Niknafs/6b50d9df9d5396a2e92e, how to solve it?
thank you!

ValueError("Invalid RGBA argument: {!r}".format(orig_c))

Hello, it seems that there is a problem about the arguments related to matplotlib-v.2.2.3.

I am attempting to test the E1 example with SCHISM-v.1.1.2. After modifying the absolute path in E1.yaml. I run the following command as Usage Examples manual:

$ runSchism analyze --config E1.yaml

but it returns warnings:

  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/bin/runSchism", line 155, in <module>
    main()
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/bin/runSchism", line 152, in main
    args.func(args)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/bin/runSchism", line 137, in run_schism
    plot_mut_clust_cellularity(args)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/SCHISM/visualize.py", line 530, in plot_mut_clust_cellularity
    alpha = 0.5)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/__init__.py", line 1867, in inner
    return func(ax, *args, **kwargs)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 5165, in fill_between
    collection = mcoll.PolyCollection(polys, **kwargs)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/collections.py", line 961, in __init__
    Collection.__init__(self, **kwargs)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/collections.py", line 170, in __init__
    self.update(kwargs)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/artist.py", line 888, in update
    for k, v in props.items()]
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/artist.py", line 882, in _update_property
    return func(v)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/collections.py", line 677, in set_color
    self.set_facecolor(c)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/collections.py", line 705, in set_facecolor
    self._set_facecolor(c)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/collections.py", line 690, in _set_facecolor
    self._facecolors = mcolors.to_rgba_array(c, self._alpha)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/colors.py", line 267, in to_rgba_array
    result[i] = to_rgba(cc, alpha)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/colors.py", line 168, in to_rgba
    rgba = _to_rgba_no_colorcycle(c, alpha)
  File "/home/ninomoriaty/anaconda3/envs/EvolCancer/lib/python2.7/site-packages/matplotlib/colors.py", line 212, in _to_rgba_no_colorcycle
    raise ValueError("Invalid RGBA argument: {!r}".format(orig_c))
ValueError: Invalid RGBA argument: 'f'

And it returns the following output documents : 0_E1_result.cluster.cellularity, 0_E1_result.HT.cpov, 0_E1_result.HT.cpov.pdf, 0_E1_result.HT.pov, 0_E1_result.HT.pvalues, 0_E1_result.mutation.cellularity.

It seems that the problem is caused by the arguments which conflict with matplotlib-2.2.3. But I am not sure about how to deal with it. And that is why I am writing an issue for some recommendation and advice.

SCHISM GUI

I saw in interesting github package that turns python command line tools into GUI's (https://github.com/chriskiehl/Gooey). Works by figuring out the inputs from argparse. Seems to work on SCHISM (didn't bother to get cairo installed though):

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