From 9928658d4bb9f32bb50de5face6b510050433a63 Mon Sep 17 00:00:00 2001 From: sdgamboa <53412049+sdgamboa@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:16:37 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20waldronl?= =?UTF-8?q?ab/bugphyzz@dbb8dddd507561f6484d05a5da8de6c225dfede8=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/attributes.html | 8 +++--- articles/bugphyzz.html | 21 ++++++++++++--- articles/checks.html | 12 ++++----- pkgdown.yml | 2 +- reference/getTaxonSignatures.html | 6 ++--- reference/importBugphyzz.html | 6 ++--- reference/makeSignatures.html | 6 ++--- reference/physiologies.html | 44 ++----------------------------- 8 files changed, 40 insertions(+), 65 deletions(-) diff --git a/articles/attributes.html b/articles/attributes.html index 47a672af..d5ac1384 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -106,14 +106,14 @@

Data about Attributes and Sources

Attributes

Ontology terms can be searched at OSLv3 and OSLv4.

-
- +
+

Sources

-
- +
+

Session info diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 043c5407..73723ff2 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -502,9 +502,22 @@

Get taxon signatures
-getTaxonSignatures(tax = "562", bp = bp)
+taxid <- as.character(taxize::get_uid("Escherichia coli"))
+#> ══  1 queries  ═══════════════
+#> ✔  Found:  Escherichia+coli
+#> ══  Results  ═════════════════
+#> 
+#> • Total: 1 
+#> • Found: 1 
+#> • Not Found: 0
+taxid
+#> [1] "562"

+

Get all signature names related to the E. coli taxid:

+
+getTaxonSignatures(tax = taxid, bp = bp)
 #>  [1] "bugphyzz:aerophilicity|aerobic"                                       
 #>  [2] "bugphyzz:aerophilicity|facultatively anaerobic"                       
 #>  [3] "bugphyzz:arrangement|paired cells"                                    
@@ -530,7 +543,7 @@ 
Get taxon signatures
 
Session information:
 

-
+
-

-
+

+
 

 

 
Check syntax
@@ -171,8 +171,8 @@ 
Uncatalogued columnsdiscard(~ all(is.na(.x))) |> 
   select(-error_type)
 DT::datatable(uncat_columns)
-
- +
+

Errors in syntax/values @@ -217,8 +217,8 @@

Errors in syntax/values#> Warning in instance$preRenderHook(instance): It seems your data is too big for #> client-side DataTables. You may consider server-side processing: #> https://rstudio.github.io/DT/server.html

-
- +
+
diff --git a/pkgdown.yml b/pkgdown.yml index 5b61572c..74822064 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: checks: checks.html bugphyzz: bugphyzz.html workflow: workflow.html -last_built: 2024-03-11T19:44Z +last_built: 2024-03-11T21:07Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index 5f10241b..b665b1e1 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -100,13 +100,13 @@

Examples

bp <- importBugphyzz() #> Importing multistate data... #> Downloading, bugphyzz_multistate.tsv. -#> Using data downloaded on 2024-03-11 19:44:39. +#> Using data downloaded on 2024-03-11 21:07:28. #> Importing binary data... #> Downloading, bugphyzz_binary.tsv. -#> Using data downloaded on 2024-03-11 19:44:49. +#> Using data downloaded on 2024-03-11 21:07:38. #> Importing numeric data... #> Downloading, bugphyzz_numeric.tsv. -#> Using data downloaded on 2024-03-11 19:44:51. +#> Using data downloaded on 2024-03-11 21:07:40. sig_names_1 <- getTaxonSignatures("562", bp) sig_names_2 <- getTaxonSignatures("Escherichia coli", bp, tax_id_type = "Taxon_name") diff --git a/reference/importBugphyzz.html b/reference/importBugphyzz.html index 1a6d68b9..9808c67d 100644 --- a/reference/importBugphyzz.html +++ b/reference/importBugphyzz.html @@ -112,11 +112,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-11 19:44:39.
+#> Using data downloaded on 2024-03-11 21:07:28.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-11 19:44:49.
+#> Using data downloaded on 2024-03-11 21:07:38.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-11 19:44:51.
+#> Using data downloaded on 2024-03-11 21:07:40.
 names(bp)
 #>  [1] "aerophilicity"                        
 #>  [2] "antimicrobial resistance"             
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html
index 3d6a73ba..e00260a6 100644
--- a/reference/makeSignatures.html
+++ b/reference/makeSignatures.html
@@ -134,11 +134,11 @@ 
Examples

     

 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-11 19:44:39.
+#> Using data downloaded on 2024-03-11 21:07:28.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-11 19:44:49.
+#> Using data downloaded on 2024-03-11 21:07:38.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-11 19:44:51.
+#> Using data downloaded on 2024-03-11 21:07:40.
 sigs <- lapply(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs)
 
diff --git a/reference/physiologies.html b/reference/physiologies.html
index c03e36a9..ebd3e93b 100644
--- a/reference/physiologies.html
+++ b/reference/physiologies.html
@@ -107,48 +107,8 @@ 
Value

     
Examples

     
l <- physiologies('all')
 #> All physiologies will be imported.
-#> Finished COGEM pathogenicity rating.
-#> Finished acetate producing.
-#> Finished aerophilicity.
-#> Finished animal pathogen.
-#> Finished antimicrobial resistance.
-#> Finished antimicrobial sensitivity.
-#> Finished arrangement.
-#> Finished biofilm forming.
-#> Finished biosafety level.
-#> Finished butyrate producing.
-#> Finished coding genes.
-#> Finished country.
-#> Finished disease association.
-#> Finished extreme environment.
-#> Finished genome size.
-#> Finished geographic location.
-#> Finished gram stain.
-#> Finished growth medium.
-#> Finished growth temperature.
-#> Finished habitat.
-#> Finished halophily.
-#> Finished health associated.
-#> Finished hemolysis.
-#> Finished host-associated.
-#> Finished hydrogen gas producing.
-#> Finished isolation site.
-#> Finished lactate producing.
-#> Finished length.
-#> Finished metabolite production.
-#> Finished metabolite utilization.
-#> Finished motility.
-#> Finished mutation rate per site per generation.
-#> Finished mutation rate per site per year.
-#> Finished optimal ph.
-#> Finished pathogenicity human.
-#> Finished plant pathogenicity.
-#> Finished shape.
-#> Finished sphingolipid producing.
-#> Finished spore formation.
-#> Finished spore shape.
-#> Finished width.
-#> Warning: Missing columns in halophily. Missing columns are: Genome_ID, Accession_ID
+#> Warning: cannot open URL 'https://doc-0c-1g-sheets.googleusercontent.com/pub/54bogvaave6cua4cdnls17ksc4/lvib3rdru8icp0jf32h2h2iu68/1710191325000/107006744893612523839/*/e@2PACX-1vR45vzAobXMOH1SCECpkBkIvxTsG5d8jAweSHaUst-gFKQcS0tTYUjivmLVByOLbFZgF59miCyF11TC?output=csv': HTTP status was '400 Bad Request'
+#> Error in file(file, "rt"): cannot open the connection to 'https://docs.google.com/spreadsheets/d/e/2PACX-1vR45vzAobXMOH1SCECpkBkIvxTsG5d8jAweSHaUst-gFKQcS0tTYUjivmLVByOLbFZgF59miCyF11TC/pub?output=csv'
 df <- physiologies('aerophilicity')[[1]]
 #> Finished aerophilicity.