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Add multimedia example datasets (se_relative, tse_relative) - #233
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Bundle three example objects (se_relative, tse_relative, tse_pathway) under data/multimedia_data_demo.rda with roxygen documentation in R/multimedia_data_demo.R, and note the addition in NEWS.
| # samples (excluding sample i itself). | ||
| sample_ids <- tse$SampleID | ||
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| tse$dysbiosis <- sapply(seq_along(tse$disease_binary), function(i) { |
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Is this "dysbiosis score" common thing? If it is, it could be added to e.g., mia::addAlpha
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Yes in a way it is. But this should be a separate issue and not postpone merging this one imo (this has taken really long time already). We could make a note there to switch to that when ready,.
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@microsud has R package dysbiosisR but only in Github I think. Maybe it could be integrated with his permission.
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Yes in a way it is. But this should be a separate issue and not postpone merging this one imo (this has taken really long time already). We could make a note there to switch to that when ready,.
I agree that this should not be postponed because of that, but as the chapter is using "dysbiosis score", reader probably wonders how to calculate them so this could be good addition
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Hi @TuomasBorman, I noticed this PR was reverted in #234 shortly after being merged. Could you let me know the reason? Do you want to complete the "dysbiosis score" part before merging? Or is there something I should fix so it can be re-submitted to miaViz? I just noticed that the data has not been included in miaViz yet. Happy to open a new PR with whatever changes are needed. Thanks! |
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Summary
Adds two example data objects for demonstrations and examples across miaViz:
se_relative—SummarizedExperimentwith relative abundance datatse_relative—TreeSummarizedExperimentwith the same data plus a phylogenetic tree