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blank bed graph visualization #154

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violacimatti opened this issue May 22, 2024 · 1 comment
Open

blank bed graph visualization #154

violacimatti opened this issue May 22, 2024 · 1 comment

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@violacimatti
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violacimatti commented May 22, 2024

Hi, this is my code to visualize a bed graph:

import gosling as gos

data= gos.csv(
    url='/violacimatti/Desktop/gosling/finale10.bedgraph',
    headerNames=['chrom','start','end','value'],
    chromosomeField='chrom',
    genomicFields=['start','end'],
    separator='\t'
)

gos.Track(data).mark_line().encode(
    x=gos.X("start:G", axis="top"),
    y=gos.Y("value:Q", axis="none"),
).view()

The problem is that when I visualize it I get a blank visualization, and it's the same also by using different bed graphs files.

@manzt
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manzt commented Jun 4, 2024

Hi there, this is very difficult to debug without a minimal reproducible example. Would you be able to share the bedgraph file? Or at least a representative sample and paste here, e.g.:

cat /violacimatti/Desktop/gosling/finale10.bedgraph | head -n 40 > data.bedgraph

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