use of dict mapping on navis.plot3d about navis

[schlegelp]

Afraid this is not how the cn_color parameter works. From help(navis.plot3d):

cn_colors :       str | tuple | dict | "neuron"
                  Overrides the default colors:

                  - single color as str (e.g. ``'red'``) or rgb tuple (e.g.
                    ``(1, 0, 0)``)
                  - dict mapping the connectors tables ``type`` column to a
                    color (e.g. `{0: (1, 0, 0)}`)
                  - with "neuron", connectors will receive the same color as
                    their neuron

Bottom line: cn_dict lets you choose whether you want e.g. presynapses in green instead of red. I will update the help to make this clearer.

For what you want to do there are two options:

1. Subset the connectors table in nl to only those synapses from/to the APL. This is a bit tricky with neuprint IIRC.
2. Fetch the synapses between APL and your neuron separately and add them as a scatter plot

An illustrative example for option 2:

Here I'm visuazing inputs from APL (425790257) onto LHMB1 (5813020988)

>>> # Fetch LHMB1
>>> nl = neu.fetch_skeletons(5813020988, with_synapses=True)
>>> # Fetch connections from APL onto LHMB1
>>> cn = neu.fetch_synapse_connections(source_criteria=neu.NeuronCriteria(bodyId=425790257), target_criteria=neu.NeuronCriteria(bodyId=5813020988))
>>> # Subset to those in the CA 
>>> cn = cn[cn.roi_post == 'CA(R)']
>>> # Get the xyz locations 
>>> locs = cn[['x_post', 'y_post', 'z_post']].values
>>> # Plot 
>>> navis.plot3d([nl, locs, ca], scatter_kws={'color': 'green', 'size': 5}, color='k')

[Gigi-prisco]

Understood, and I have managed to get the plot I was looking for. Just one further issue, the color='k' piece makes both my neuron and the calyx roi black. How can I change the color of the skeleton while keeping the roi in its typical light grey.

Thank you very much for your help

[schlegelp]

Hmm... It shouldn't do that. What version of navis are you using?

[schlegelp]

>>> import navis
>>> print(navis.__version__)

[Gigi-prisco]

Thanks for literally reading my mind while I was trying to look for that. it says 0.5.2

[schlegelp]

Try updating: the most recent version is 0.5.3.

pip3 install navis -U

Also what browser are you using? I had some issues with plotly plots in Safari in the past.

[schlegelp]

Also note that you will have to restart the Python kernel in your notebook and re-run your code for the update to take effect.

[Gigi-prisco]

It worked! Once again, thank you!
One last question. Would all this work on a mesh instead of a skeleton? If yes, can I just substitute neu.fetch_skeletons with neu.fetch_mesh_neuron to do that?

[schlegelp]

Yep

[schlegelp]

@Gigi-prisco can this issue be closed?