Looking for the best plot for overlapping features

Question

[ste.lu]

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!

[Sej Modha]

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

Answer 1

[predeus]

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.