I would like to use an IPython notebook as a way to interactively analyze some genome charts I am making with Biopython’s GenomeDiagram
module. While there is extensive documentation on how to use matplotlib
to get graphs inline in IPython notebook, GenomeDiagram uses the ReportLab toolkit which I don’t think is supported for inline graphing in IPython.
I was thinking, however, that a way around this would be to write out the plot/genome diagram to a file and then open the image inline which would have the same result with something like this:
gd_diagram.write("test.png", "PNG") display(file="test.png")
However, I can’t figure out how to do this – or know if it’s possible. So does anyone know if images can be opened/displayed in IPython?
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Answer
Courtesy of this post, you can do the following:
from IPython.display import Image Image(filename='test.png')