@jasmainak Sure thing!

There is:
plot_morphology in Cell
plot_cell_morphology in Viz
plot_cells in Network
plot_cells in Viz

The plotting is being done in Viz as the methods plot_cells and plot_cell_morphology, with Network and Cell each having their own corresponding accessor methods.

So currently, plot_cells is redundantly repeating code that could be performed by plot_cell_morphology, however, plot_cell_morphology is too specific to be used for this process.

So the goal is to take the general 'cell plotting' code in plot_cell_morphology and plot_cells, and move it to a new private method (ex. _plot_cell), therein calling this new private method in both plot_cell_morphology and plot_cells.

@jasmainak Do I have that right?

Additionally, the plot_cells method has the same name in Network as it does in Viz, however, plot_morphology in Cell has a different name than it does in Viz: plot_cell_morphology. Wouldn't it be best to standardize this among the pairs? If so, do you prefer they have the same name or different?

So currently, plot_cells is redundantly repeating code that could be performed by plot_cell_morphology

nopes, they are different visualizations:

what I am imagining is something like this:

or

as in this paper: https://www.sciencedirect.com/science/article/pii/S1053811920309526

Btw, all the visualization functions are put in one file so that the code is all in one place and redundancy is avoided between functions. Then they are called from the methods of the classes. Sometimes it's nice to have a different name. For example if you a plotting method for Dipole, then you want to do:

dipole.plot()

but in viz.py it's better to have more specific names because there might be several plotting functions and all of them cannot be called plot. You could for e.g., call it plot_dipole in viz.py

Ahh yes I understand.

So you want a new method (ex. _plot_cell_type_morphologies), which calls plot_cell_morphology, that iterates through the cell types and creates models for each one. This new method would then be called in plot_cells to create the cell model visualization alongside the network visualization.

@jasmainak is that right?

I would create a separate function/method. You can always combine it with other visualizations by creating subplots. E.g.:

fig, axes = plt.subplots(2, 1)
net.plot_morphology(ax=axes[0])
net.plot_cells(ax=axes[1])

I'm sorry I had forgotten that a plot_cells method already existed. Now, move the common logic between net.plot_morphology and cell.plot_morphology to a private function so that there is minimum repetition in the code.

Btw, all the visualization functions are put in one file so that the code is all in one place and redundancy is avoided between functions. Then they are called from the methods of the classes. Sometimes it's nice to have a different name. For example if you a plotting method for Dipole, then you want to do:

dipole.plot()

but in viz.py it's better to have more specific names because there might be several plotting functions and all of them cannot be called plot. You could for e.g., call it plot_dipole in viz.py

This I understand now, makes perfect sense.

I would create a separate function/method. You can always combine it with other visualizations by creating subplots. E.g.:

fig, axes = plt.subplots(2, 1)
net.plot_morphology(ax=axes[0])
net.plot_cells(ax=axes[1])

Sounds good!

I'm sorry I had forgotten that a plot_cells method already existed. Now, move the common logic between net.plot_morphology and cell.plot_morphology to a private function so that there is minimum repetition in the code.

I thought plot_cells plotted the network visualization? In addition, there is no such net.plot_morphology function, in my version of hnn-core.

My understanding was that you wanted me to create a plot_cells_morphology function, and move the common logic between plot_cells_morphology and plot_cell_morphology to a shared private function.

I think I have a pretty good understanding of what needs to be done. If it's alright with you, let me give it a shot, and we can move this conversation to a PR @jasmainak .

I thought plot_cells plotted the network visualization?

yes. I mean that I confused you in the original post by using that name since that function is already for a different purpose.

Give it a shot and we can discuss more there!