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Statistical testing and visualization of mult-set intersections
Hi,
Thanks for the package. It is very useful, flexible, and well-documented.
I am currently comparing 9 sets which results in 511 combinations of intersection. I want to select specific intersections to plot (which can be achieved by sorting the data in a pre-defined order), but I cannot figure out how to select the number of bars to show. Say, I'm interested in plotting only the first 10 bars. How would I do that? I would appreciate any suggestions.
Best,
Lucas
Dear Minghui,
It's me again. I wanted to kindly ask for a favour. Since I would like to visually present the expected vs. the observed overlap in the generic barplot output of SuperExactTest, I wanted to ask if there is an easy way to add this feature, e.g. by overlaying the observed value bars with semitransparent bars showing the expected overlap. I tried to do this myself but have difficulties to implement your nice feature to show the comparison by colored bullets underneath the bars.
Thanks a lot.
Best, Martin
Dear Minghui,
thanks a lot for your great software, which has helped me a lot. Unfortunately, I recently ran into a problem when using the SuperExactTest with a large background population (n=1238970). Irrespective of the version used (I also tried 1.0.5), R crashed because of a segmentation fault caused by c stack overflow.
Is there anything I can do myself to fix this or is there another simple solution to this? I have accordingly attached a test dataset that caused the problem.
Thanks a lot for your help,
cheers, Martin
example.tar.gz
Dear mw201608,
Thank you for the development and active maintaining of SuperExactTest
Under this combination of values, log.scale is not applied to the show.expected.overlap white bars. They end up rescaling outside of the ylim shown upon applying log.scale.
Is this something that can be tested/confirmed? Maybe I am not having something alright. Happy to send input files in any case.
plot(res, Layout="landscape", sort.by='p-value', log.scale=T, show.expected.overlap=T,
elements.list=t1, elements.rot=0, show.elements=T, color.on='black', color.off='white',
legend.text.cex=2.0, ylim = c(0, 2000),
show.expected.overlap=TRUE, expected.overlap.style="box", expected.overlap.lwd=0.4,
overlap.size.cex=1.0, intersection.size.rotate=T, flip.vertical=F)
Best regards,
Hi,
In the following attached example I get a memory error. Is there any obvious reason for this? I have observed this ~3-4 times in 20 cases that I have run in bulk.
https://www.dropbox.com/s/cw534rczhwy34pe/debugCaseSuperExactTest.rds?dl=0
events <- readRDS('debugCaseSuperExactTest.rds') # total = 1010
total <- 1010 # this is the number of rows in the original dataframe
res=supertest(events, n=total)
*** Error in `/g/scb/zaugg/rio/miniconda2/lib/R/bin/exec/R': double free or corruption (!prev): 0x0000000002598720 ***
======= Backtrace: =========
Thanks!
Ignacio
Hi,
thanks for developing this nice tool!
I ran into a problem when I was trying to export the plot into pdf. A multi-pages plots were generated with same figure. I think this is only the case for the landscape layout.
Could you please take a look into the issue?
Many thanks!
Rui
I'm a bit of a novice coder, so this is an overlap of a general "how to" question, and a question specific for this package.
I intend to use this software to look for the overlap between 6 different lists. I am grateful for how simple and approachable this was. However, 6 lists lends itself to 57 (63-6) hypotheses tested on over laps.
Very simply, I would like to run multiple hypothesis test correction on the results of the analysis AND plot these results using the plot functions outlined in the vignettes.
The closest I have been able to get is saving the summary table as its own variable and then adding a new column with the adjusted p values.
res_table <- summary(res)$Table res_table$padj <- stats::p.adjust(res_table %>% pull(., P.value), method = "BH", n = length(res_table %>% pull(., P.value)))
But now that this is a separate table and not the S3 class object, it is incompatible with plot function. How do i add these adjusted p values to the S3 class object and then select to plot those instead of the P.value column?
Thank you for the help!
Dear mw201608,
Thank you for the development of this package.
I am intersecting multiple datasets and I would like to combine them using the UpSet visualization. For this I would like to save them as PDFs before editing. However, I get the following error when executing plot.msets
on the res
object instance:
pdf(pdf_path, width=w, height=h)
plot.msets(res)
dev.off()
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), :
Viewport has zero dimension(s)
Is there an example for saving PDFs? So far I just see an example for PNGs.
Thank you,
Ignacio
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