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lwaldron merged 2 commits into from
Nov 8, 2026
Merged

Parameterize the articles on data version; add the attributes supplementary table #4

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Parameterize the articles on data version; add the attributes supplem…
lwaldron Nov 8, 2026
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Attributes table: checks, out_dir param, warn when validation may not…
lwaldron Nov 8, 2026
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12 changes: 10 additions & 2 deletions inst/rmd/bsdb_signatures.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,9 @@ title: "High-throughput ORA with BSDB signatures"
output:
html_document:
toc: true
params:
bugphyzz_version: "devel"
uberon_obo: "https://github.com/obophenotype/uberon/releases/download/v2024-05-13/uberon-basic.obo"
---

```{r, include = FALSE}
Expand Down Expand Up @@ -84,7 +87,12 @@ dim(bsdb)
BugSigDB subsets by body site:

```{r, message=FALSE}
uberon <- getOntology(onto = "uberon")
## Uberon, pinned to the release current when these analyses were first run
## (May 2024). bugsigdbr::getOntology() fetches the latest release and its
## download step fails on some networks, so the OBO is read directly.
uberon <- ontologyIndex::get_ontology(
params$uberon_obo, propagate_relationships = c("is_a", "part_of")
)
bsdb_subsets_by_bodysite <- vector("list", length(body_sites))
names(bsdb_subsets_by_bodysite) <- body_sites
for (i in seq_along(bsdb_subsets_by_bodysite)) {
Expand All @@ -102,7 +110,7 @@ for (i in seq_along(bsdb_subsets_by_bodysite)) {
Bugphyzz:

```{r, message=FALSE}
bp <- importBugphyzz(v = 0.8)
bp <- importBugphyzz(version = params$bugphyzz_version) # manuscript thresholds (MCC 0.7, R2 0.5) are the defaults
names(bp)
```

Expand Down
108 changes: 85 additions & 23 deletions vignettes/articles/data_integration_and_stats.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@ output:
html_document:
code_folding: hide
toc: true
params:
bugphyzz_version: "devel" # Zenodo DOI of the release the paper cites, or "devel"
validation_tsv: "" # path or URL of a taxPProValidation validation_summary.tsv; "" uses the copy in the installed bugphyzz
out_dir: "" # where the supplementary TSVs are written; "" means tempdir()
---

```{r script options, include = FALSE}
Expand Down Expand Up @@ -38,26 +42,26 @@ library(cowplot)
## Bugphyzz data

```{r import bp, message=FALSE}
discrete_types <- c(
"binary", "multistate-intersection", "multistate-union"
)
bp <- importBugphyzz(v = 0.5) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID))) |>
map(~ {
attr_type <- unique(.x$Attribute_type)
if (attr_type %in% discrete_types) {
df <- .x |>
filter(
!(Validation < 0.7 & Evidence == "asr")
)
} else if (attr_type == "numeric") {
df <- .x |>
filter(
!(Validation < 0.5 & Evidence == "asr")
)
}
df
})
## importBugphyzz() keeps imputed (ASR) annotations with MCC >= 0.7
## (discrete) or R2 >= 0.5 (numeric) by default, the manuscript thresholds;
## since bugphyzzExports 2026-11 the exported files are already filtered.
bp <- importBugphyzz(version = params$bugphyzz_version) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID)))
## Cross-validation table (taxPProValidation): the installed package's copy
## unless params$validation_tsv points to another version
validation <- if (nzchar(params$validation_tsv)) {
readr::read_tsv(params$validation_tsv, show_col_types = FALSE)
} else {
if (params$bugphyzz_version != "devel") {
warning(
"validation_tsv is empty, so Figure 2 and the attributes table use ",
"the validation_summary.tsv shipped with bugphyzz ",
packageVersion("bugphyzz"), ", which may not be the version the ",
params$bugphyzz_version, " release was filtered with."
)
}
bugphyzz:::.validationData() # bugphyzz exports no accessor for this table
}

@claude claude Bot Nov 8, 2026

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Without validation_tsv, the validation table comes from the installed bugphyzz via the internal bugphyzz:::.validationData(), not from the release named by bugphyzz_version. If you pass a DOI and leave validation_tsv empty, Figure 2 and the new Supplementary Table 2 can show MCC/R2 values from a different version than the annotation counts next to them. Nothing warns about this.

Suggested fixes:

  • Make validation_tsv required whenever bugphyzz_version != "devel", or stop() / warning() when the two are inconsistent.
  • Replace ::: with an exported accessor. Bioconductor guidelines discourage :::, and an internal rename would silently break the vignette. If no accessor exists, export one in bugphyzz.

length(bp)
```
```{r}
Expand Down Expand Up @@ -131,7 +135,7 @@ attr_asr_default_names <- map(bp, ~ {

attr_asr_default <- length(attr_asr_default_names)

attr_asr_all <- bugphyzz:::.validationData() |>
attr_asr_all <- validation |>
filter(rank == "all") |>
select(physiology, mcc_mean, r2_mean) |>
pull(physiology) |>
Expand All @@ -148,7 +152,7 @@ count_summary_tbl <- tibble::tribble(
"Number of annoations from sources", n_annotations_source,
"Number of IBD annotations", n_annotations_ibd,
"Number of annotations imputed through ASR", n_annotations_asr,
"Number of attributes with ASR data (default > 0.5 val)", attr_asr_default,
"Number of attributes with ASR data passing validation", attr_asr_default,
"Number of attributes with ASR data (all)", attr_asr_all
)

Expand Down Expand Up @@ -235,7 +239,7 @@ Create plot of MMC values for discrete attributes:
```

```{r validation discrete}
val <- bugphyzz:::.validationData() |>
val <- validation |>
filter(rank == "all") # Validation including taxa of mixed ranks as input (keyword is "all")
dis_phys_names <- val |>
filter(!is.na(mcc_mean)) |>
Expand Down Expand Up @@ -597,6 +601,64 @@ sources <- read.table(
myDataTable(sources, page_len = nrow(sources))
```

# Supplementary Table: attributes

One row per attribute: type, unit, number of sources, annotations by evidence
(curated from a source, IBD = inherited from strains by taxonomy, ASR), taxa,
and the cross-validation score of each attribute value at rank "all" (MCC for
discrete, R2 for numeric; those at or above the export threshold, 0.7 and
0.5, have imputed annotations in the release).

```{r supp table attributes}
val_str <- validation |>
filter(rank == "all") |>
mutate(
score = ifelse(is.na(mcc_mean), r2_mean, mcc_mean),
label = ifelse(
physiology == attribute, sprintf("%.2f", score),
sprintf("%s %.2f", attribute, score)
)
) |>
group_by(physiology) |>
summarise(`Validation (rank all)` = paste(label, collapse = "; "), .groups = "drop") |>
mutate(Attribute = tolower(physiology)) |> # the export lowercases attribute names
select(-physiology)
supp_attr_tbl <- bp |>
map(~ {
.x |>
summarise(
Type = unique(Attribute_type)[1],
Unit = if ("Unit" %in% names(.x)) paste(unique(na.omit(Unit)), collapse = ";") else "",
Sources = n_distinct(Attribute_source[!is.na(Attribute_source)]),
Curated = sum(Evidence %in% c("exp", "igc", "tas", "nas")),
IBD = sum(Evidence == "tax"),
ASR = sum(Evidence == "asr"),
Total = n(),
Taxa = n_distinct(NCBI_ID)
Comment on lines +629 to +637

@claude claude Bot Nov 8, 2026

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The new supplementary table has no test or check. Total is n() while Curated + IBD + ASR counts only specific Evidence codes, so any other or NA Evidence value makes the columns stop summing to Total without notice. The join to validation is by tolower(Attribute), so a mismatch gives silent NA in the validation column.

Suggested fixes:

  • Add stopifnot(with(supp_attr_tbl, all(Curated + IBD + ASR == Total))) after the table is built.
  • Assert that every row has a validation string, or document which attributes are expected to be NA.
  • Note that Sources / Type use unique(...)[1], which hides inconsistent values within an attribute.

)
}) |>
bind_rows(.id = "Attribute") |>
mutate(.key = tolower(Attribute)) |>
left_join(val_str, by = c(".key" = "Attribute")) |>
select(-.key) |>
arrange(desc(Total))
## every annotation is curated, IBD or ASR, and every attribute with ASR
## annotations has a validation score to show for them
stopifnot(
all(supp_attr_tbl$Curated + supp_attr_tbl$IBD + supp_attr_tbl$ASR == supp_attr_tbl$Total),
!any(supp_attr_tbl$ASR > 0 & is.na(supp_attr_tbl$`Validation (rank all)`))
)
myDataTable(supp_attr_tbl, page_len = nrow(supp_attr_tbl))
```

```{r write supp tables, include = FALSE}
## TSV copies for the manuscript supplement
out_dir <- if (nzchar(params$out_dir)) params$out_dir else tempdir()
readr::write_tsv(supp_attr_tbl, file.path(out_dir, "supplementary_table_attributes.tsv"))
readr::write_tsv(sources, file.path(out_dir, "supplementary_table_sources.tsv"))
message("Supplementary tables written to ", out_dir)
```
Comment on lines +654 to +660

@claude claude Bot Nov 8, 2026

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This chunk writes TSVs to the knit working directory. That is a side effect on the source tree when built with R CMD build/BiocCheck, and the location varies with how the article is rendered (rmarkdown::render vs pkgdown). It also uses an unnamed relative path, and supplementary_table_sources.tsv is not mentioned in the PR's table list.

Fix: take an output directory from a param (e.g. params$out_dir, defaulting to tempdir()), build the path with file.path(), and use readr::write_tsv (readr is already in Imports). Also add *.tsv outputs to .gitignore/.Rbuildignore if they can land in the repo.


# Session information

```{r class.soruce = 'fold-show'}
Expand Down
35 changes: 14 additions & 21 deletions vignettes/articles/enrichment_dbbact.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,9 @@ title: "Enrichment with dbBact approach"
output:
html_document:
toc: yes
params:
bugphyzz_version: "devel" # Zenodo DOI of the release the paper cites, or "devel"
uberon_obo: "https://github.com/obophenotype/uberon/releases/download/v2024-05-13/uberon-basic.obo"
---

```{r, include = FALSE}
Expand Down Expand Up @@ -41,26 +44,11 @@ freq_var <- 1
Import bugphyzz and create signatures at the genus and species levels:

```{r, warning=FALSE, message=FALSE}
discrete_types <- c(
"binary", "multistate-intersection", "multistate-union"
)
bp <- importBugphyzz(v = 0.5) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID))) |>
map(~ {
attr_type <- unique(.x$Attribute_type)
if (attr_type %in% discrete_types) {
df <- .x |>
filter(
!(Validation < 0.7 & Evidence == "asr")
)
} else if (attr_type == "numeric") {
df <- .x |>
filter(
!(Validation < 0.5 & Evidence == "asr")
)
}
df
})
## importBugphyzz() keeps imputed (ASR) annotations with MCC >= 0.7
## (discrete) or R2 >= 0.5 (numeric) by default, the manuscript thresholds;
## since bugphyzzExports 2026-11 the exported files are already filtered.
bp <- importBugphyzz(version = params$bugphyzz_version) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID)))
bpSigs_g <- map(bp, ~ {
makeSignatures(
dat = .x, taxIdType = "NCBI_ID", taxLevel = "genus",
Expand Down Expand Up @@ -96,7 +84,12 @@ dim(bsdb)
Subset by body site:

```{r}
uberon <- getOntology(onto = "uberon")
## Uberon, pinned to the release current when these analyses were first run
## (May 2024). bugsigdbr::getOntology() fetches the latest release and its
## download step fails on some networks, so the OBO is read directly.
uberon <- ontologyIndex::get_ontology(
params$uberon_obo, propagate_relationships = c("is_a", "part_of")
)
bsdb_subsets_by_bodysite <- vector("list", length(body_sites))
names(bsdb_subsets_by_bodysite) <- body_sites
for (i in seq_along(bsdb_subsets_by_bodysite)) {
Expand Down
29 changes: 8 additions & 21 deletions vignettes/articles/nychanes.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@ output:
html_document:
toc:
true
params:
bugphyzz_version: "devel" # Zenodo DOI of the release the paper cites, or "devel"
---

```{r, include = FALSE}
Expand Down Expand Up @@ -89,26 +91,11 @@ tse_gn
bugphyzz data:

```{r, message=FALSE}
discrete_types <- c(
"binary", "multistate-intersection", "multistate-union"
)
bp <- importBugphyzz(v = 0.5) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID))) |>
map(~ {
attr_type <- unique(.x$Attribute_type)
if (attr_type %in% discrete_types) {
df <- .x |>
filter(
!(Validation < 0.7 & Evidence == "asr")
)
} else if (attr_type == "numeric") {
df <- .x |>
filter(
!(Validation < 0.5 & Evidence == "asr")
)
}
df
})
## importBugphyzz() keeps imputed (ASR) annotations with MCC >= 0.7
## (discrete) or R2 >= 0.5 (numeric) by default, the manuscript thresholds;
## since bugphyzzExports 2026-11 the exported files are already filtered.
bp <- importBugphyzz(version = params$bugphyzz_version) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID)))

aer <- bp$aerophilicity
dim(aer)
Expand Down Expand Up @@ -366,7 +353,7 @@ tibble(
### dbBact - genus - BugSigDB 727

```{r}
bsdb <- importBugSigDB() |>
bsdb <- importBugSigDB(version = "10.5281/zenodo.10627578") |> # v1.2.1, as in the other articles
as_tibble()
tob_sigs <- bsdb |>
filter(`BSDB ID` %in% c("bsdb:727/1/1", "bsdb:727/1/2")) |>
Expand Down
27 changes: 7 additions & 20 deletions vignettes/articles/subgingival_plaque.Rmd
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Expand Up @@ -3,6 +3,8 @@ title: "BSEA gingival plaque - MicrobiomeBenchmarkData - 35S"
output:
html_document:
toc: true
params:
bugphyzz_version: "devel" # Zenodo DOI of the release the paper cites, or "devel"
---

```{r include = FALSE}
Expand Down Expand Up @@ -51,26 +53,11 @@ table(tse_subset$body_subsite)
Signatures at the genus level:

```{r bp signatures genus, message = FALSE}
discrete_types <- c(
"binary", "multistate-intersection", "multistate-union"
)
bp <- importBugphyzz(v = 0.5) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID))) |>
map(~ {
attr_type <- unique(.x$Attribute_type)
if (attr_type %in% discrete_types) {
df <- .x |>
filter(
!(Validation < 0.7 & Evidence == "asr")
)
} else if (attr_type == "numeric") {
df <- .x |>
filter(
!(Validation < 0.5 & Evidence == "asr")
)
}
df
})
## importBugphyzz() keeps imputed (ASR) annotations with MCC >= 0.7
## (discrete) or R2 >= 0.5 (numeric) by default, the manuscript thresholds;
## since bugphyzzExports 2026-11 the exported files are already filtered.
bp <- importBugphyzz(version = params$bugphyzz_version) |>
map(~ mutate(.x, NCBI_ID = as.character(NCBI_ID)))
aer <- bp$aerophilicity
gn_sigs <- makeSignatures(
dat = aer, taxIdType = 'Taxon_name', taxLevel = 'genus'
Expand Down
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