update all files

DESCRIPTION

@@ -51,36 +51,36 @@ Depends:
 Imports: 
     dplyr,
     utils,
-    magrittr,
     purrr,
-    rlang,
     stringr,
-    taxize,
     tidyr,
     tidyselect,
-    tibble,
-    crayon,
-    mgsub,
-    methods,
-    tidytext,
-    taxizedb,
     BiocFileCache,
     tools
 Suggests: 
     DT,
     forcats,
     ggplot2,
     htmltools,
+    taxizedb,
     knitr,
     rmarkdown,
     sessioninfo,
+    taxize,
     testthat,
     EnrichmentBrowser,
     MicrobiomeBenchmarkData,
     mia,
     stats,
+    rlang,
     limma,
+    mgsub,
+    methods,
     readr,
+    crayon,
+    tibble,
+    magrittr,
+    tidytext,
     BiocStyle
 URL: https://github.com/waldronlab/bugphyzz
 BugReports: https://github.com/waldronlab/bugphyzz/issues

R/bugphyzz.R

@@ -1,3 +1,5 @@
+# utils::globalVariables(c("Rank"))
+Rank <- NULL
 #' Import bugphyzz
 #'
 #' \code{importBugphyzz} imports bugphyzz annotations as a list of

R/physiologies.R

@@ -249,7 +249,7 @@ showPhys <- function(which_names = 'all') {
 ## helper function for .importSpreadsheets
 .DISCRETE_ATTRIBUTE_TYPES <- function() {
   fname <- system.file('extdata', 'spreadsheet_links.tsv', package = 'bugphyzz')
-  dat <- read.table(file = fname, header = TRUE, sep = '\t')
+  dat <- utils::read.table(file = fname, header = TRUE, sep = '\t')
   unique(dat[dat$trait_type == 'discrete',]$attribute_type)
 }
 
@@ -333,14 +333,14 @@ showPhys <- function(which_names = 'all') {
 ## Append links to error table
 .appendLinks <- function(x) {
   fname1 <- system.file('extdata/spreadsheet_links.tsv', package = 'bugphyzz')
-  links <- read.table(fname1, header = TRUE, sep = '\t')
+  links <- utils::read.table(fname1, header = TRUE, sep = '\t')
   select_cols <- c("physiology", "source_link")
-  phys_links <- links %>%
+  phys_links <- links |>
     dplyr::select(tidyselect::all_of(select_cols))
-  custom_links <- .customLinks() %>%
+  custom_links <- .customLinks() |>
     dplyr::select(tidyselect::all_of((select_cols)))
   links <- dplyr::bind_rows(phys_links, custom_links)
-  x %>%
+  x |>
     dplyr::left_join(links, by = c("dataset" = "physiology"))
 }
 

vignettes/bugphyzz.Rmd

@@ -299,22 +299,19 @@ knitr::kable(gsea_tbl)
 
 To retrieve all signature names associated with a specific taxon,
 users can utilize the `getTaxonSignatures` function.
-It's important to note that only taxids should be used as input for this
-function.
 
 Let's see an example using _Escherichia coli_ (taxid: 562).
 
-Get taxid for _E. coli_ using taxize:
+Get all signature names associated to _E. coli_:
 
 ```{r, message=FALSE}
-taxid <- as.character(taxize::get_uid("Escherichia coli"))
-taxid
+getTaxonSignatures(tax = "Escherichia coli", bp = bp)
 ```
 
 Get all signature names associated to the _E. coli_ taxid:
 
 ```{r}
-getTaxonSignatures(tax = taxid, bp = bp)
+getTaxonSignatures(tax = "562", bp = bp)
 ```
 
 # Session information