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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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UpSet plot misses to show some overlaps/cuts off shown overlaps at 40 #226

Open CPerscheid opened 2 years ago

CPerscheid commented 2 years ago

Hi there, I have created an UpSet plot that shows overlaps of 17 sets. However, I noticed that the sums of the overlaps are smaller than the original set sizes. For example, see "ANOVA" at the bottom of the plot: It contains 25 entities, but the overlaps shown only add up to 16.

Screenshot 2021-12-16 at 21 53 49

I am creating the UpSet plot via "fromList(rankings)", where rankings is a list of the entity-lists, and the resulting data set (which is then forwarded to the upset command) contains the right number of "1" for ANOVA (i.e. 25 as the set size). However, this is not reflected in the plot. I do not get this discrepancy with smaller set numbers.

I have already updated to the most recent version via devtools, however the problem persists.

Please help!

Best,

Cindy

CPerscheid commented 2 years ago

Is there maybe an upper limit of overlaps that is shown on the plot? I noticed the plot never shows more than 40 bars for overlaps, and plots that work fine (i.e., where the overlaps sum up to the correct set sizes) do not reach 40 bars - could it be that there is an upper limit for bars, and remaining bars (if we have more than 40 overlaps) are just cut off?

DaianeH commented 2 years ago

Same thing is happening to me in two different projects I'm trying to use UpSet for.

zhongzheng1999 commented 1 year ago

@DaianeH @CPerscheid Hello, you may want to set the parameter nintersects as large as possible. Late reply, hope to help you. hahah~~