blank visualization

[violacimatti]

Hi, I have a .bw file of which I would like to visualize the mark bar, however, following also the tutorials, I always get a blank graph.
The following is the code:
`import gosling as gos

data = gos.bigwig(
url='/Users/violacimatti/Desktop/gosling/MB110_H3K27me3.bw',
column='position',
value='peak',
binSize=8
)

track = gos.Track(data).mark_bar().encode(
x='position:G',
y='peak:Q',
size=gos.value(20),
color=gos.value('blue')
).properties(width=725, height=180, layout='linear')

vis = track.view(title='group 4')
vis.save('group4.html')

`

[sehilyi]

Thank you for reaching out! The code looks good to me, and if I replace the URL with the one we have on gosling.js.org, it shows the visualization:

(Note that I replaced the last line (vis.save('group4.html')) with vis since .save exports the HTML file without rendering anything)

• You can find the code on this Colab Link: https://colab.research.google.com/gist/sehilyi/36b2b20b39d46bd8ddc94b4f82454b3b/multiple-coordinated-views.ipynb

Have you tried to open the group4.html file that you created as well?

[violacimatti]

Yes but as soon as I insert a local file path instead of an actual url it just gives me a blank graph

[sehilyi]

Hmm, I see. I wonder if data cannot be accessed by Gos. Could you try directly accessing the data that is hosted on the local server? When you print the data, you should be able to see the URL to your local data, something like

{'type': 'csv',
 'url': 'http://localhost:49967/resources/2529389-UCSC.HG38.Human.CytoBandIdeogram.bed',
 'headerNames': ['chrom', 'chromStart', 'chromEnd', 'name', 'stain'],
 'chromosomeField': 'chrom',
 'genomicFields': ['chromStart', 'chromEnd'],
 'separator': '\t'}

Opening the URL (e.g., http://localhost:49967/resources/2529389-UCSC.HG38.Human.CytoBandIdeogram.bed in my case) using your browser should download the file if it is accessible.

[violacimatti]

Yes, this works, but if try this code:

import` gosling as gos 
import clodius as clodius 

data = gos.bigwig(
    url='http://localhost:8080/MB113_H3K27me3.BigWig',  
    column='position',
    value='peak',
    binSize=8
)

track = gos.Track(data).mark_area().encode(
    x='position:G',
    y='peak:Q',
    size=gos.value(2),
    color=gos.value('royalblue')
).properties(width=725, height=180, layout='linear')

vis = track.view(title='WNT')
vis.save('WNT.html')`

And then open the html file from the local server, this is what I get: