Unable to draw more than one gene in the same plot

[fbrundu]

Hi,
I receive the following error while trying to draw a list of genes, probably due to changes in the underlying matplotlib API:

c.draw(['GRIA1', 'SLC1A3']);

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-36-4449e82bda2b> in <module>()
----> 1 c.draw(['GRIA1','SLC1A3']);

/Users/user/.pyenv/versions/2.7.15/Python.framework/Versions/2.7/lib/python2.7/site-packages/scTDA/main.pyc in draw(self, color, connected, labels, ccmap, weight, save, ignore_log, table, axis, a)
   1230             values = [(1.0-colorb[node]/bmax, max(1.0-(colorr[node]/rmax+colorb[node]/bmax), 0.0),
   1231                        1.0-colorr[node]/rmax) for node in pg.nodes()]
-> 1232             networkx.draw_networkx_nodes(pg, pos, node_color=values, node_size=sizes)
   1233             polca = [(colorr[node], colorb[node]) for node in pg.nodes()]
   1234         elif type(color) == list and len(color) == 3:

/Users/user/.pyenv/versions/2.7.15/Python.framework/Versions/2.7/lib/python2.7/site-packages/networkx/drawing/nx_pylab.pyc in draw_networkx_nodes(G, pos, nodelist, node_size, node_color, node_shape, alpha, cmap, vmin, vmax, ax, linewidths, edgecolors, label, **kwds)
    412                                  linewidths=linewidths,
    413                                  edgecolors=edgecolors,
--> 414                                  label=label)
    415 
    416     node_collection.set_zorder(2)

/Users/user/.pyenv/versions/2.7.15/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/__init__.pyc in inner(ax, *args, **kwargs)
   1853                         "the Matplotlib list!)" % (label_namer, func.__name__),
   1854                         RuntimeWarning, stacklevel=2)
-> 1855             return func(ax, *args, **kwargs)
   1856 
   1857         inner.__doc__ = _add_data_doc(inner.__doc__,

/Users/user/.pyenv/versions/2.7.15/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes/_axes.pyc in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, **kwargs)
   4277                 raise ValueError("c of shape {} not acceptable as a color "
   4278                                  "sequence for x with size {}, y with size {}"
-> 4279                                  .format(c.shape, x.size, y.size))
   4280         else:
   4281             colors = None  # use cmap, norm after collection is created

AttributeError: 'list' object has no attribute 'shape'

c is an UnrootedGraph initialized through Ayasdi.

Versions

scTDA==0.97
matplotlib==2.2.2
networkx==2.1

---

Francesco

[fbrundu]

I solved by installing graphviz and pygraphviz (homebrew and pip):

brew install graphviz
pip install --install-option="--include-path=/usr/local/include/" --install-option="--library-path=/usr/local/lib/" pygraphviz

[fbrundu]

Actually I just found that works only with some list of genes and not with others..

Update

It works with

c.draw([['GRIA1', 'SLC1A3']]);

but not with

c.draw(['GRIA1', 'SLC1A3']);