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Installing Magic

Installing magic

Recently a method for imputing single cell gene expression matricies was posted on biorxiv by David van Dijk et al., called magic (Markov Affinity-based Graph Imputation of Cells). I’ve been analysing single cell RNA-seq data recently, and this method looks like it could be useful when trying to find co-transcriptional networks, as single cell data suffers from dropout which makes finding co-transcriptional networks hard.

I had lots of problems getting magic installed and running, so will document them here for future reference.

Firstly, there seems to be an error in the setup.py script where it looks for a non-existent /data directory that should contain test data. Running pip3 install . as instructed in the readme resulted in an error, and I have raised an issue on github. Commenting out the last few lines of the setup.py script seemed to provide a temporary fix.

The next problem was getting Tk to work properly with python. Tk is a GUI toolkit and not park of python itself. Chances are that Tk is installed somewhere on your computer, and the problem is that python doesn’t know where it is. After trying lots of different things, the solution I found was to install python3 using the mac installer and launching IDLE, as this finds and links the Tk installation with python at runtime. From the python website:

The Python for Mac OS X installers downloaded from this website dynamically link at runtime to Tcl/Tk macOS frameworks.

I then found the path of the newly installed python3 (it was symlinked to /usr/local/bin/python3 for me) and used this to create a new virtualenv:

mkvirtualenv -p /usr/local/bin/python3 py3

I then installed magic again in the virtualenv (from the github repo):

pip3 install .

Next I installed all the jupyter stuff. It’s important to link the right ipython kernel to the jupyter notebook, otherwise it will seem like you still don’t have access to Tk, even though at this point you can sucessfully import tkinter in python3. To do this, install jupyter, ipython, the ipython kernel, and then link the kernel:

pip install jupyter ipython ipykernel
python3 -m ipykernel install --user

Now you should be able to import magic without any problems, and use it in a jupyter notebook. You can also start the GUI by running the magic_gui.py script:

python3 magic_gui.py