Tutorial pbmc4k

[camilliano]

Hello,
I am trying the SPRING new version.
I have some trouble with the tutorial pbmc 4K.

The preprocessing is OK but when I try to ,visualize I have a lot of issues...

So I run this in the SPRING_dev-master folder:
python -m CGIHTTPServer 8080

then:


(idem with springViewer_1_5) and I have this on the terminal:

127.0.0.1 - - [15/May/2018 15:19:20] code 404, message File not found
127.0.0.1 - - [15/May/2018 15:19:20] "GET /datasets/pbmc4k/graph_data.json HTTP/1.1" 404 -
127.0.0.1 - - [15/May/2018 15:19:20] code 404, message File not found
127.0.0.1 - - [15/May/2018 15:19:20] "GET /favicon.ico HTTP/1.1" 404 -
127.0.0.1 - - [15/May/2018 15:19:21] code 404, message File not found
127.0.0.1 - - [15/May/2018 15:19:21] "GET /favicon.ico HTTP/1.1" 404 -
127.0.0.1 - - [15/May/2018 15:20:40] "GET /springViewer_1_5_dev.html?datasets/pbmc4k/full HTTP/1.1" 200 -
127.0.0.1 - - [15/May/2018 15:20:40] code 404, message File not found
127.0.0.1 - - [15/May/2018 15:20:40] "GET /datasets/pbmc4k/full/mutability.txt HTTP/1.1" 404 -
127.0.0.1 - - [15/May/2018 15:20:40] code 404, message File not found
127.0.0.1 - - [15/May/2018 15:20:40] "GET /datasets/pbmc4k/selected_cells.txt HTTP/1.1" 404 -

FYI in pbmc4k folder there is :
/counts_norm.npz
/counts_norm_sparse_cells.hdf5
/counts_norm_sparse_genes.hdf5
/genes.txt
/total_counts.txt

and folder /full with
/categorical_coloring_data.json
/cell_filter.npy
/cell_filter.txt
/color_data_gene_sets.csv
/color_stats.json
/coordinates.txt
/edges.csv
/graph_data.json
/intermediates.npz
/run_info.json

What did I miss?

Thanks you for your help!

Camille

[swolock]

Hi Camille,

I'm not sure of the problem, but here a couple things to check:

1. Does the folder SPRING_dev-master/datasets/pbmc4k/full/ exist?

2. Are are you using the following URL to (try to) view the SPRING plot?
   http://localhost:8080/springViewer_1_5_dev.html?datasets/pbmc4k/full

By the way, it is normal to see a few "File not found" messages, but not for graph_data.json.

Best,
Sam

[camilliano]

Yes the folder does exist and yes I am using the right url...

[swolock]

Ok, a few more questions for you:

1. What happens when you try to load the URL? Does anything get displayed?
2. What browser are you using? We usually use Chrome on Mac and Chrome or Edge on Windows. In Chrome, it's often best to use incognito mode to make sure everything is getting properly refreshed.
3. Can you share any messages printed in the javascript console? (in Chrome: View>Developer>JavaScript Console)

[camilliano]

when I load the URL
http://localhost:8080/springViewer_1_5_dev.html?datasets/pbmc4k/full : nothing
http://localhost:8080/springViewer_1_6_dev.html?datasets/pbmc4k/full : I only have a network but I can't use any functions or "play" with the network.
I am on Firefox in linux environment.

[swolock]

I see. We've never tested this on Linux, so it's possible that's the issue. Can you tell me what gets printed in the web console (Ctrl+Shift+K) when you try to load the URL?

[camilliano]

The early version works just fine..
Sorry for the copied/pasted, here is what I obtained:

"Pixi.js 4.5.1 - WebGL - http://www.pixijs.com/"  pixi.min.js:16:11030
datasets/pbmc4k  forceLayout_script.js:540:5
datasets/pbmc4k/full  forceLayout_script.js:541:5
Got the data  forceLayout_script.js:547:13
# genes =  33694  colorBar.js:666:4
ANIM  forceLayout_script.js:416:2
Gene =    colorBar.js:534:5
Gene =  CD3D  colorBar.js:534:5
Read gene data:  530  colorBar.js:180:21
Gene =  CD3D  colorBar.js:534:5
Read gene data:  168  colorBar.js:180:21
Gene =  CD3D  colorBar.js:534:5
Read gene data:  166  colorBar.js:180:21
Gene =  CD3D  colorBar.js:534:5
Read gene data:  128  colorBar.js:180:21
Gene =  LYZ  colorBar.js:534:5
Read gene data:  180  colorBar.js:180:21
Gene =  LYZ  colorBar.js:534:5
Read gene data:  156  colorBar.js:180:21

[swolock]

Great, that narrows it down a bit. Do you see a file called "tmplog2" in SPRING_dev-master? It should be created when you try to enter a gene name to view. If it's there, can you share its contents? I've pasted a "successful" example below; yours is probably breaking somewhere along the way.

import cgi -- 0.047
import numpy -- 1.141
import h5py -- 0.555
got cgi data -- 0.000
CD3D
got cell filter-- 0.008
loaded hdf5 data -- 0.022
inialized array -- 0.000
filled array -- 0.000
filtered array -- 0.000
returned data -- 0.003
1.78184390068

Similarly would you mind telling me what happens when you enter cgi-bin/grab_one_gene.py in the terminal?

[camilliano]

Here is what I have in the "tmplog2" file

import cgi -- 0.013
import numpy -- 0.064

And here just to show you what my windows looks like:

[swolock]

It looks like python is failing to import h5py. Since you were able to run the example notebook, which also uses h5py, it appears that you are using a different python environment to run your local server. I would try installing h5py in this environment, or activating the same the environment you used in the notebook before starting the local server.

[camilliano]

I will try this, thanks for the advice. I will tell you the results...
Here is cgi-bin/grab_one_gene.py output

Traceback (most recent call last):
  File "cgi-bin/grab_one_gene.py", line 45, in <module>
    update_log(logf, gene)
  File "cgi-bin/grab_one_gene.py", line 16, in update_log
    o.write(logdat + '\n')
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

[QiangShiPKU]

I have the similar issues.

• It seems not to obtain any information of genes. http://localhost:8000/springViewer_1_6_dev.html?/datasets/pbmc4k/full
  

• This is my "tmplog2" file

import cgi -- 0.009
import numpy -- 0.071
import h5py -- 0.031
got cgi data -- 0.000
CD3D

• My output is the same as @camilliano for cgi-bin/grab_one_gene.py

• My "tmplogenrich" file is empty.

[AllonMKlein]

Can you send all the relevant files? Including those needed to run the SPRINGplot making script as well as the SPRING plot that was outputted.

…

On Mon, Aug 13, 2018 at 3:16 AM, Qiang ***@***.***> wrote: I have the similar issues. - It seems not to obtain any information of genes. http://localhost:8000/ springViewer_1_6_dev.html?/datasets/pbmc4k/full <http://localhost:8000/springViewer_1_6_dev.html?/datasets/pbmc4k/full> [image: image] <https://user-images.githubusercontent.com/40571792/44023013-e255537a-9f1b-11e8-93d1-574e53a7c27d.png> - This is my "tmplog2" file import cgi -- 0.009 import numpy -- 0.071 import h5py -- 0.031 got cgi data -- 0.000 CD3D - My output is the same as @camilliano <https://github.com/camilliano> for cgi-bin/grab_one_gene.py - My "tmplogenrich" file is empty. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AUBd7e4pWkv54OmIHAOabzpuCnghu4DDks5uQUPigaJpZM4T_khY> .

[QiangShiPKU]

@AllonKleinLab This is my relevant files
https://www.dropbox.com/s/21l76jcf9yd88iq/pbmc4k.zip?dl=0

[swolock]

@QiangShiPKU I was able to load your SPRING plot successfully. I think the issue may be the "/" at the beginning of the path in your URL. Can you try using this one instead?
http://localhost:8000/springViewer_1_6_dev.html?datasets/pbmc4k/full

[QiangShiPKU]

@swolock yeah...I was so negligent. Many thanks for your hospitality