Make tutorial nice about scirpy

[grst]

In GitLab by @grst on Mar 20, 2020, 18:18

• assign labels to Leiden clusters (maybe based on original publication)

[grst]

In GitLab by @grst on Mar 21, 2020, 13:38

[grst]

In GitLab by @szabogtamas on Mar 25, 2020, 18:18

When loading the 3K dataset, I get the folowing error:
~/.conda/envs/scTCR/lib/python3.7/site-packages/tqdm/notebook.py in status_printer(_, total, desc, ncols)
97 else: # No total? Show info style bar with no progress tqdm status
---> 98 pbar = IProgress(min=0, max=1)
99 pbar.value = 1

NameError: name 'IProgress' is not defined

[grst]

In GitLab by @grst on Mar 25, 2020, 19:13

Quick fix is to pip install ipywidgets.

The underlying problem is somewhere in scanpy, or even the progressbar module itself.
Will think about how to work around.

[grst]

In GitLab by @grst on Mar 25, 2020, 19:35

See scverse/scanpy#1130

[grst]

In GitLab by @szabogtamas on Mar 25, 2020, 19:46

That was fast.

[grst]

In GitLab by @grst on Mar 25, 2020, 19:49

Well, have you seen the diff? It's literally 5 characters deleted :D

[grst]

In GitLab by @szabogtamas on Mar 25, 2020, 19:51

I tried to install iwidgets, but did not solve the issue. Now I get "Internal server error", so I will just leave it for today.
I will probably install the packages locally tomorrow and try there.
Hope I can run the tutorial notebook, locally at least. When the vdj_plot branch is merged, I might play around with the tutorial notebook.

[grst]

In GitLab by @grst on Mar 25, 2020, 19:53

I will add a fix for the progressbar tomorrow morning.

[grst]

In GitLab by @grst on Mar 26, 2020, 08:02

This should be fixed in the mater branch now per !26 - no more need for ipywidgets.

[grst]

In GitLab by @szabogtamas on Mar 26, 2020, 10:35

Cannot test now due to server error of Jupyterhub

[grst]

In GitLab by @grst on Mar 26, 2020, 18:24

Make sure images are rendered the correct size:

[grst]

In GitLab by @grst on Mar 27, 2020, 12:33

mentioned in merge request !28

[grst]

In GitLab by @grst on Mar 29, 2020, 09:38

mentioned in merge request !29

[grst]

In GitLab by @grst on Mar 30, 2020, 11:15

mentioned in merge request !31

[grst]

In GitLab by @grst on Mar 30, 2020, 17:48

mentioned in merge request !32

[grst]

In GitLab by @grst on Mar 31, 2020, 11:54

[grst]

In GitLab by @grst on Mar 31, 2020, 17:16

VDJ usage for a single clonotypes:

I think here the plot with the full combinations makes more sense. We should add that to the tutorial.

[grst]

#107 closes most points. But of course improving and keeping the tutorial up-to-date is a continuous process.