Suggestion: Include an example to extract gene combinations from UpSetR output
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 72/100
- Issue type
- Documentation
- Clarity
- Clearly specified
- Activity status
- Stale
- Tech stack
- r
- Domain
- documentation
Research direction
Open the UpSetR section in the project documentation, choosing the relevant book or vignette mentioned in the issue. Add the supplied example for extracting gene combinations and readable labels, then verify that it renders clearly and demonstrates the resulting list structure for downstream analysis.
Written by the indexing model from the issue text.
Description
Hi! First of all, thank you for the great work on the package <3. I'm currently using it for a gene expression analysis comparing experimental groups, and I encountered a recurring need: extracting the specific gene lists that correspond to each combination shown in the UpSet plot.
I’d like to propose adding the following example to the documentation (book or vignette) under the UpSetR section, as it could benefit researchers working with biological datasets—particularly those dealing with transcriptomics or pathway analysis.
# Obtain set names
set_names <- set_name(m1)
# Get binary names of combinations
comb_bin <- comb_name(m1)
# Create list with subsets by combination
comb_sets <- lapply(comb_name(m1), function(nm) extract_comb(m1, nm))
# Generate readable names for combinations
comb_labels <- sapply(comb_bin, function(bin) {
active <- as.logical(as.integer(strsplit(bin, "")[[1]]))
paste(set_names[active], collapse = ",")
})
# Assign these names to the list
names(comb_sets) <- comb_labels
str(comb_sets) # list 15
This approach provides a modular and interpretable way to bridge the visual output of the plot with downstream analyses like enrichment testing (e.g., GO or KEGG). It's especially useful when prioritizing subsets based on their biological relevance or visual prominence in the plot.
Thanks for considering this addition—and again, congrats on the great tool!
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