Add table of ontology.

waldronlab · Jun 11, 2024 · d8f8cf2 · d8f8cf2
1 parent 558397c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: bugphyzzAnalyses
 Type: Package
 Title: Analyses performed with the bugphyzz package
-Version: 0.1.18
+Version: 0.1.19
 Authors@R:
     c(
         person(

diff --git a/vignettes/articles/enrichment_dbbact.Rmd b/vignettes/articles/enrichment_dbbact.Rmd
@@ -205,7 +205,7 @@ obs_sigs_g <- getPairedSigs(obs_dat_dec, obs_dat_inc, rank = "genus", cat = TRUE
 
 Enrichment at the species level:
 
-```{r, fig.height=10, fig.width=20}
+```{r, fig.height=12, fig.width=25}
 obs_feces_enriched_s <- dbEn2(
     obs_sigs_s$dec, obs_sigs_s$inc, term_list = bpSigs_s,
     perm = perm_var, freq = 1
@@ -222,7 +222,28 @@ row_dat_list$obs_feces_sp <- obs_feces_enriched_s |>
         Condition = "Obesity",
         Rank = "species"
     )
-dbHt(obs_feces_enriched_s, scm = FALSE, col_pad = 20)
+dbHt(obs_feces_enriched_s, scm = TRUE)
+```
+
+```{r, eval=FALSE, echo=FALSE}
+# tbl <- colData(obs_feces_enriched_s) |> 
+#     as.data.frame() |> 
+#     as_tibble()
+# 
+# classif <- taxizedb::classification(tbl$Taxon, db = "ncbi")
+# dat <- map(classif, ~ {
+#     .x |> 
+#         filter(rank == "phylum") |> 
+#         select(Phylum = name)
+# }) |> 
+#     bind_rows()
+# 
+# col_data <- bind_cols(tbl, dat)
+# 
+# col_data |> 
+#     count(Condition, Phylum) |> 
+#     arrange(Condition, -n) 
+
 ```
 
 ```{r, fig.width=20, fig.height=8}

diff --git a/vignettes/articles/validation.Rmd b/vignettes/articles/validation.Rmd
@@ -17,7 +17,7 @@ library(ggrepel)
 library(bugphyzzAnalyses)
 ```
 
-## Import validation data
+# Import validation data
 
 Validation scripts and outputs are in: https://github.com/waldronlab/taxPProValidation/tree/main
 
@@ -89,7 +89,80 @@ myDataTable(output, page_len = nrow(output))
 ```
 
 
-## Session information
+# Ontology data
+
+```{r}
+fname <- system.file(
+    "extdata", "attributes.tsv", package = "bugphyzz"
+)
+o <- readr::read_tsv(fname, show_col_types = FALSE)
+```
+
+
+```{r}
+o2 <- o |> 
+    mutate(ontology = gsub("(?<!CO)_(?!(\\d+:\\d+))", ":", ontology, perl = TRUE)) |>
+    mutate(ontology = sub("^(.*):.*$", "\\1", ontology)) |> 
+    select(ontology) |> 
+    filter(!is.na(ontology)) |> 
+    arrange(ontology) |> 
+    distinct()
+o3 <- o2 |> 
+    mutate(
+        Description = case_when(
+            ontology == "APO" ~ "obophenotype/ascomycete-phenotype-ontology",
+            ontology == "ARO" ~ "Antibiotic Resistance Ontology",
+            ontology == "BTO" ~ "The BRENDA Tissue Ontology",
+            ontology == "CO_320" ~ "The Planteome Project",
+            ontology == "CO_331" ~ "The Planteome Project",
+            ontology == "CO_345" ~ "The Planteome Project",
+            ontology == "CO_357" ~ "The Planteome Project",
+            ontology == "ECOCORE" ~ "An ontology of core ecological entities",
+            ontology == "EFO" ~ "Experimental Factor Ontology",
+            ontology == "EHDAA2" ~ "Ontobee/Human developmental anatomy, abstract",
+            ontology == "ENM" ~ "eNanoMapper ontology",
+            ontology == "ENVO" ~ "The Environment Ontology",
+            ontology == "ERO" ~ "Eagle-I Research Resource Ontology",
+            ontology == "FMA" ~ "The Foundational Model of Anatomy",
+            ontology == "FOODON" ~ "Ontobee/Food Ontology",
+            ontology == "GO" ~ "Gene Ontology",
+            ontology == "IDO" ~ "Infectious Disease Ontology",
+            ontology == "IDOMAL" ~ "Malaria Ontology",
+            ontology == "MCO" ~ "Microbial Conditions Ontology",
+            ontology == "MICRO" ~ "Ontology of Prokaryotic Phenotypic and Metabolic Characters",
+            ontology == "MONDO" ~ "Mondo Disease Ontology",
+            ontology == "MP" ~ "The Mammalian Phenotype Ontology",
+            ontology == "NCBITaxon" ~ "NCBI organismal classification",
+            ontology == "NCIT" ~ "NCI Thesaurus OBO Edition",
+            ontology == "OBI" ~ "Ontology for Biomedical Investigations",
+            ontology == "OHMI" ~ "OHMI: Ontology of Host-Microbiome Interactions",
+            ontology == "OMIT" ~ "Ontology for MIRNA Target",
+            ontology == "OMP" ~ "Ontology of Microbial Phenotypes",
+            ontology == "Orphanet" ~ "Orphanet",
+            ontology == "PATO" ~ "PATO - the Phenotype And Trait Ontology",
+            ontology == "PHIPO" ~ "Pathogen Host Interactions Phenotype Ontology",
+            ontology == "PO" ~ "Plant Ontology",
+            ontology == "SIO" ~ "Ontobee/Semanticscience Integrated Ontology",
+            ontology == "SNOMED" ~ "SNOMED CT (International Edition)",
+            ontology == "SPD" ~ "The Spider Anatomy Ontology",
+            ontology == "SYMP" ~ "Symptom Ontology",
+            ontology == "UBERON" ~ "Uber-anatomy ontology",
+            ontology == "UPa" ~ "Unipathway",
+            ontology == "XCO" ~ "Experimental condition ontology",
+            ontology == "ZFA" ~ "Zebrafish Anatomy Ontology (ZFA)"
+        )
+    ) |> 
+    mutate(
+        ontology = case_when(
+            grepl("^(CO_).*$", ontology) ~ "CO",
+            TRUE ~ ontology
+    )) |> 
+    distinct() |>
+    dplyr::rename(Ontology = ontology)
+myDataTable(o3)
+```
+
+# Session information
 
 ```{r, echo=FALSE}
 sessioninfo::session_info()