Visualizing on Jupyter (higlass-python)

[DhTandon]

I am implementing hi-glass python on Jupyter, and upon running the test data code: from higlass.client import View, Track from higlass.tilesets import cooler

ts1 = cooler('../data/Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool') tr1 = Track('heatmap', tileset=ts1) view1 = View([tr1]) display, server, viewconf = higlass.display([view1])

display

I get the error message stating:

Error Retrieving tileset info: http://localhost:60501/spi/v1

Please advise on the correcting. The code above has been copied from the HiGlass webpage https://docs.higlass.io/jupyter.html

Hence when I try to run the code with my own data, it gives the same error

[flekschas]

Error Retrieving tileset info: http://localhost:60501/spi/v1

Are you sure this is the link? /spi should be /api. Have you tried opening this link in a browser window?

Also, have you made sure you installed all the requirements? https://github.com/higlass/higlass-python#requirements

[LIZW2019]

hi,

I have come across the same problem. I have all the requirements install susscessfully. I can load the data you provided successfully at the first example at the tutorial, but when i load my own cool, I saw this messange. What should I do? Is it related to the memory or the thread when I use jupyter?

[pkerpedjiev]

Hey @LIZW2019 , sorry for the delayed reply. Could you provide an short snippet of the code you're trying to run as well as the version of higlass-python?

import higlass
print(higlass.__version__)

[LIZW2019]

Hey @LIZW2019 , sorry for the delayed reply. Could you provide an short snippet of the code you're trying to run as well as the version of higlass-python?

import higlass
print(higlass.__version__)

Yes, my pleasure. my version is 0.4.0, and my code is as follow

from higlass.client import View, Track
from higlass.tilesets import cooler
import higlass

ts1 = cooler('DpnII_run01_TAIR10.matrix.cool')
tr1 = Track('heatmap', tileset=ts1)
view1 = View([tr1])
display, server, viewconf = higlass.display([view1])

display

And the result looks like

Look forward to your reply!

[pkerpedjiev]

Can you verify that the cooler you're trying to load is a multires cooler? If not could you try doing:

cooler zoomify --balance DpnII_run01_TAIR10.matrix.cool

And then try loading the resulting file in the same manner as before?