Create multimedia.qmd #768

YihanLiu4023 · 2025-07-14T17:36:48Z

No description provided.

antagomir

Thanks!

Check the suggestions and the following:

increase support for the mia and (Tree)SummarizedExperiment methods when possible, this is very useful for compatibility with many other methods; I added suggestions. Also multimedia seems to support SE so this should be done.
Let us try to avoid repetition in the code; this has now two almost identical parts. Shall we prepare example data that is readily usable for the examples?
I am wondering if there would be a way to combine the two mediation chapters into one?
If we consider these methods widely usable we should consider providing wrappers for the interpretation, summaries, and visualizations of the results; either as contributions to "multimedia" package, or into mia or some other pkg (doesn't matter which pkg as long as it works)

inst/pages/multimedia.qmd

antagomir · 2025-08-06T19:23:15Z

Could you resolve the cases you have closed (from the "Resolve" buttons)?

YihanLiu4023 · 2025-08-06T20:06:07Z

Fixed most of the detailed comments, still working on the more genral ones like creating pkg. Will finish this asap

antagomir · 2025-08-17T20:25:09Z

Can you resolve the completed suggestions above and confirm if this is ready to merge?

Just fixed some minor inconsistence in the name of variables

antagomir · 2025-09-17T21:14:16Z

To be checked in more detail before merge, regarding the following:

May require additional wrapper functions to extract the relevant information from data objects more intuitively (but those should be in multimedia pkg or mia, so not sure if it is feasible to do as part of this PR - but if not, then it is unclear when this would take place).
Are the examples now sufficiently short & concise (data cleaning steps usually avoided in OMA examples; some explanations could be added instead).

YihanLiu4023 · 2025-09-18T22:22:16Z

To be checked in more detail before merge, regarding the following:

May require additional wrapper functions to extract the relevant information from data objects more intuitively (but those should be in multimedia pkg or mia, so not sure if it is feasible to do as part of this PR - but if not, then it is unclear when this would take place).

Are the examples now sufficiently short & concise (data cleaning steps usually avoided in OMA examples; some explanations could be added instead).

Hi Leo, thank you for the suggestions. I have added some wrapper functions, especially to where you indicated. For the data cleanning steps, do you mean we can remove those part, and add some texts to explain instead?

antagomir · 2025-09-19T07:07:13Z

The data cleaning part would work best if we include a suitable cleaned demo data in the R pkg, then we can skip the data cleaning steps in OMA. The problem is that if we could do this with every single method but then more than half of the book might easily be data cleaning examples, and this is also shifting the focus from the actual method to general data processing steps -> can we include demo data set/s in the multimedia, mia, or other pkg, or can we use already existing demo data sets?

antagomir · 2025-09-19T07:07:47Z

Regarding the wrappers, we could see if we can include these in a package if they would be generally useful anyway.

himelmallick · 2025-09-19T10:31:06Z

Hi Leo – just wanted to quickly chime in here. This dataset is a special case where we don’t have a conventional, well-defined outcome for mediation analysis. Instead, the outcome is a dysbiosis score derived from taxonomic profiles, as described by Lloyd-Price et al. (2019), which, to my knowledge, hasn’t been implemented elsewhere. We are already drawing the data from curatedMetagenomicData, but creating the dysbiosis score is a necessary step to showcase the mediation analysis.

antagomir · 2025-09-20T21:01:55Z

Thanks. I think that dysbiosis score could then stay there. Let's check @TuomasBorman feedback.

TuomasBorman

Thanks, looks very good! However, there are couple points to discuss.

This book is intended as teaching material to demonstrate specific analyses and tasks. The main focus is on the underlying ideas and concepts rather than implementation details. Therefore, the code is kept as simple as possible to achieve the intended outcomes. More polished analyses, including advanced plots, are better suited for workflow packages (we are also considering creating workflow package to showcase more complex analyses).

There are couple lengthy code chunks that do operations to results. Having these long chunks have opposite effect as readers are exhausted by the amount of code and they cannot focus on the main points. Everything that is not relevant for the main point should be removed even though plots or names would not be optimal.

Ideally, these wrappers will be implemented in a package, but of course it takes some time. At least, we should have plan to implement them. If we just leave it here, these will be never implemented as we are very busy with everything.

inst/pages/multimedia.qmd

antagomir · 2025-11-19T11:30:22Z

Can you @YihanLiu4023 confirm when you're ready with the updates? Can you also press the "Update branch" button above to ensure that this PR is in sync with the latest devel branch.

YihanLiu4023 · 2025-11-20T23:37:59Z

Updated file submitted!

antagomir

Thanks - some points to clarify still.

Overall this looks good but it will be essential to consider the following:

Data cleaning operations should be either ignored, or readily cleaned demo data set should be used (it can be placed to one of our packages). Otherwise OMA would be primarily a data cleaning example collection..
We need to check if any ready-made functionality is available to fetch and visualize results from mediation analyses. Now this is done with custom code. Maybe multimedia package has some utilities and if not, we should see if some tasks are so central that they should be standardized (either into multimedia package as contributed PR, or into mia).

inst/pages/multimedia.qmd

antagomir · 2025-11-21T21:27:31Z

inst/pages/multimedia.qmd

+# Calculate dysbiosis score for each sample
+# For each sample i, we compute the median distance between sample i and all reference samples in `ref_set`
+sample_ids <- tse[["SampleID"]]
+
+tse[["dysbiosis"]] <- sapply(seq_along(tse$disease_binary), function(i) {
+
+  # Logical vector indicating all other reference samples (excluding i)
+  ref_others <- tse$disease_binary & (sample_ids != sample_ids[i])
+
+  # Compute median distance between sample i and these reference samples
+  median(diss[i, ref_others], na.rm = TRUE)
+
+})


Can you check if the functions from the dysbiosis package could be applicable here?

I noticed that the dysbiosisR package do have a similar function called "dysbiosisMedianCLV()", but it can only be applied to objects in phyloseq. I can use the function "mia::convertToPhyloseq()" for convertion but just want to make sure if we want this convertion, since it's a little bit complex as well

We do not want to convert to phyloseq. We could probably add SE support for this package relatively easily but maybe it is better not wait for that. Unless @microsud wants to comment on this?

inst/pages/multimedia.qmd

antagomir · 2025-11-21T21:32:32Z

inst/pages/multimedia.qmd

+# Create the Mediation Data object
+exper <- mediation_data(
+  se_relative,
+  outcomes   = "dysbiosis",
+  treatments = "treatment",
+  mediators  = medi_idx
+)


The multimedia package already seems to have support for SummarizedExperiment that we are using. Just confirming, is it really necessary to convert SE into Mediation Data object?

I think it is necessary to convert SE into a Mediation Data object, as confirmed by the multimedia tutorial.

Right, I thought that it could be so. In that case we can keep this but at the same time an issue should be opened (to OMA?) to propose PR to multimedia to add direct SE support (the extra conversion step can be probably automated).

inst/pages/multimedia.qmd

antagomir · 2025-11-21T21:37:43Z

inst/pages/multimedia.qmd

+# Clean the pathway names
+pwy <- rownames(summary_df)
+pwy <- gsub("PWY0\\.", "PWY0-", pwy) # PWY0.xxx → PWY0-xxx
+pwy <- gsub("PWY\\.", "PWY-", pwy) # PWY.xxx → PWY-xxx
+pwy <- gsub("\\.", " ", pwy) # leftover dots → spaces
+pwy <- gsub("__", ": ", pwy) # double underscores → colon
+pwy <- gsub("_\\.", " ", pwy) # underscore then dot → space
+pwy <- gsub("_", " ", pwy) # remaining underscores → space
+pwy <- gsub("\\.\\.", " ", pwy) # double dots → space
+pwy <- gsub("\\.$", "", pwy) # remove ending period
+# pwy <- trimws(pwy) # final cleanup
+rownames(summary_df) <- pwy


Can we prepare demo data in one of the R packages (e.g. mia) that is sufficiently clean?

OMA is dedicated to show how methods work, and data cleaning is something that is so common that it will overwhelm all examples in the book if we are not actively avoiding it.

Yes, I can do that. Do I just need to create a new pull request to the mia package for the cleaned demo data?

Yes, a PR. It should follow similar conventions than the other demo data sets.

antagomir · 2025-11-21T21:38:28Z

inst/pages/multimedia.qmd

+ggplot(summary_df, aes(x=estimate, y=reorder(mediator, estimate), color=significant)) +
+  geom_point() +
+  geom_errorbarh(aes(xmin=lower, xmax=upper), height=0.2) +
+  geom_vline(xintercept=0, linetype="dashed", color="grey") +
+  theme_classic() +
+  labs(
+    x = "Observed Indirect Effect with Bootstrap CI",
+    y = "Mediator",
+    title = "Forest Plot of Mediation-specific Indirect Effects for Pathway"
+  ) +
+  scale_color_manual(values=c("black","red")) +
+  theme(legend.position="bottom")
+


Can we consider having default visualization method for mediation analyses, for isntance in miaViz pkg (if not multimedia pkg itself)?

We can add a package-native mediator visualization using plot_mediators(), which shows the observed outcome–mediator relationships (colored by treatment) for the top pathwise indirect effects. Here is the example plots for species:

(Mediators are standardized (z-scored) for comparability across features; hence values may be negative. Besides, many microbial features are sparse; several mediators exhibit near-zero values for most samples, producing vertical bands.)

While a miaViz-based visualization would instead emphasize the taxonomic/pathway abundance structure (e.g., distributions/compositional patterns) rather than mediation-effect estimates, our original bootstrap forest plot complements plot_mediators() by summarizing effect uncertainty via CIs across mediators. Do you want plot_mediators() to be the primary/default visualization (with the forest plot as optional), or should we keep both as complementary views?

plot_mediators() sounds good - in which R/Bioc package this would be placed? Some programming conventions could be considered depending on the answer.

Create multimedia.qmd

c5308a5

antagomir requested changes Jul 14, 2025

View reviewed changes

Merge branch 'devel' into patch-1

e34fab9

Update multimedia.qmd

af9fafe

Merge branch 'devel' into patch-1

f2279a9

YihanLiu4023 and others added 2 commits August 30, 2025 02:36

Update multimedia.qmd

fb8c080

Just fixed some minor inconsistence in the name of variables

Merge branch 'devel' into patch-1

9151c30

YihanLiu4023 added 2 commits September 19, 2025 02:49

Merge branch 'devel' into patch-1

a51caaf

Update multimedia.qmd

9981a19

TuomasBorman requested changes Sep 23, 2025

View reviewed changes

TuomasBorman and others added 2 commits September 23, 2025 18:17

Merge branch 'devel' into patch-1

39e2659

Merge branch 'devel' into patch-1

a6415ca

Update multimedia.qmd

d2be914

Merge branch 'devel' into patch-1

505d743

antagomir reviewed Nov 21, 2025

View reviewed changes

Create multimedia.qmd #768

Are you sure you want to change the base?

Create multimedia.qmd #768

Uh oh!

Conversation

YihanLiu4023 commented Jul 14, 2025

Uh oh!

antagomir left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

antagomir commented Aug 6, 2025

Uh oh!

YihanLiu4023 commented Aug 6, 2025

Uh oh!

antagomir commented Aug 17, 2025

Uh oh!

antagomir commented Sep 17, 2025

Uh oh!

YihanLiu4023 commented Sep 18, 2025

Uh oh!

antagomir commented Sep 19, 2025

Uh oh!

antagomir commented Sep 19, 2025

Uh oh!

himelmallick commented Sep 19, 2025

Uh oh!

antagomir commented Sep 20, 2025

Uh oh!

TuomasBorman left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

antagomir commented Nov 19, 2025

Uh oh!

YihanLiu4023 commented Nov 20, 2025

Uh oh!

antagomir left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

antagomir left a comment •

edited

Loading