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hms-dbmi / UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
https://cran.rstudio.com/web/packages/UpSetR
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Feature request: manually specify intersection sizes #184

Open b-tierney opened 4 years ago

b-tierney commented 4 years ago

Hi,

I have a dataset containing 5 groups, each with tens of millions of entries, for which I've already computed overlap sizes externally. Converting my data to a binary matrix would be difficult due to its scale. Is it possible for me to manually enter in the intersection sizes (eg Group A-B: 100000, Group A-C: 15000....etc) somewhere and still use UpSetR's plotting format?

Thanks, Braden

chaouiya commented 4 years ago

I have the same requirement. Rather than providing the 'raw' data, I want to use the information of the intersections of my sets. Is this feasible with UpSerR, and how? Many thanks! Claudine

RichardJActon commented 4 years ago

I think that the implementation of upset plots in the complexheatmap package may permit you to construct set intersection objects which do not require explicit representation of the entire matrix:

https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html

chaouiya commented 4 years ago

Thank you for the answer. If I’m not mistaken, the complexheatmap implementation allows 3 types of input, all considering an explicit listing of the set contents: 1) A list of sets where each set is a vector 2) A binary matrix/data frame where rows are elements and columns are sets 3) The set can be genomic intervals

best Claudine

On 10 Apr 2020, at 21:12, Richard James Acton notifications@github.com wrote:

I think that the implementation of upset plots in the complexheatmap package may permit you to construct set intersection objects which do not require explicit representation of the entire matrix:

https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hms-dbmi/UpSetR/issues/184#issuecomment-612176999, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJSEE2P3XAV6SI7LZB5MOJDRL5VSJANCNFSM4K7X5QHQ.

RichardJActon commented 4 years ago

Ah yes - I thought that you might be able to construct your own 'comb_mat' object with the summary information that you had already computed instead of using the provided constructor methods. However, the 'comb_mat' objects do actually appear to contain a complete matrix, the properties of which are used in the plotting function not just summary info. looks like you may have to make your own plotting function if you want summary data input, or wait for an implementation here or over at complexheatmap