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Looking for the best plot for overlapping features

Hi All,

I am looking for a way to plot a big spreadsheet of genomic features.

The table has this structure:

Promoter.id1  Promoter_flanking_region.id1  Enhancer.id1  FLI1.id1  GATA1.id1  GATA2.id1  TAL1.id1  CTCF.id1  Exons.id1  Intron.id1
0             0                             0             0         0          0          0         0         1          0
0             0                             0             0         0          0          0         0         1          0
0             0                             0             0         0          0          0         0         0          1
0             1                             0             0         0          0          0         0         1          0
1             0                             1             0         0          0          0         1         0          0
0             0                             0             0         0          0          0         0         1          0
0             0                             0             0         0          0          0         0         1          0
0             0                             0             0         0          0          0         0         1          0
0             0                             0             0         0          0          0         0         1          0
0             1                             0             0         0          0          0         0         1          0

I'd like to show what is the distribution of the features in the spreadsheet and for this I was thinking about a pie chart, but some features are overlapping and that is an info I'd like to keep.

Do you have any suggestion on the best way represent these data?

Thank you!

plot suggestion
• 1,405 views • link
updated by Ram Ram • written by ste.lu ste.lu

There may be a way to deal with this in the excel spreadsheet but I doubt if anyone on this platform may be able to help you with that. I'd suggest importing this spreadsheet in either R or python pandas dataframe to perform exploratory analysis.

PS: It is not clear what is the question you are asking here, please read: Brief Reminder On How To Ask A Good Question

• 0 views • link
written by Sej Modha Sej Modha

1 answer

So there's this tool that basically is used for interactive expression analysis: http://genome.ifmo.ru/phantasus-dev/

But you can use it to do heatmap-based visualization of nearly anything.

Cluster your table using k-means and then sort by cluster. You should get a pretty good idea of feature overlap etc.

• 0 views • link
written by predeus predeus

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