Comments (4)
I tried it and saw the same odd behavior -- do_scatter
doesn't display a plot by itself, and if you add pyplot.show()
afterward, the plot shows up in a new window.
Something like this worked exactly once for me, but not repeatably:
import cnvlib
from cnvlib.commands import do_scatter
from matplotlib import pyplot
pyplot.ion()
cnr = cnvlib.read("~/code/cnvkit-examples/build/TR_95_T.cnr")
cns = cnvlib.read("~/code/cnvkit-examples/build/TR_95_T.cns")
do_scatter(cnr, cns, show_chromosome="chr12")
pyplot.show()
from cnvkit.
The following now work for me in IPython Notebook 2.3 (though I can't say which change fixed it since the initial bug report):
%pylab inline
from cnvlib import commands
commands.create_heatmap("test/formats/amplicon.cns")
show()
(shows the heatmap inline in the notebook)
import cnvlib
commands.do_scatter(cnvlib.read("test/formats/amplicon.cnr"), cnvlib.read("test/formats/amplicon.cns"))
show()
(shows the scatter plot)
Can you, or anyone else, confirm that this is OK now?
from cnvkit.
Sorry for the late reply. Both plots seem to be working well for me in ipython notebooks.
from cnvkit.
Great to hear. Thanks!
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