diff --git a/NAMESPACE b/NAMESPACE index 21af9e0f..b98c0377 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,7 +4,6 @@ export(check_valid_ncbi_ids) export(fattyAcidComposition) export(getTaxonSignatures) export(importBugphyzz) -export(importVal) export(makeSignatures) export(physiologies) export(showPhys) diff --git a/R/bugphyzz.R b/R/bugphyzz.R index 8bfd7f67..3ac3539e 100644 --- a/R/bugphyzz.R +++ b/R/bugphyzz.R @@ -53,7 +53,11 @@ importBugphyzz <- function( output <- purrr::map(output, ~ { .x |> dplyr::mutate( - Attribute = ifelse(.data$Attribute == "plant pathogenity", "plant pathogenicity", .data$Attribute) + Attribute = ifelse( + .data$Attribute == "plant pathogenity", + "plant pathogenicity", + .data$Attribute + ) ) }) @@ -187,27 +191,6 @@ getTaxonSignatures <- function(tax, bp, ...) { return(output) } - - -#' Import validation data -#' -#' \code{importValidation} impots the result of the 10-fold cross-validation. -#' -#' @return A data.frame. -#' @export -#' -#' @examples -#' -#' val <- importValidation() -#' -importVal <- function() { - url <- "https://raw.githubusercontent.com/waldronlab/taxPProValidation/main/validation_summary.tsv" - readr::read_tsv(url, show_col_types = FALSE) |> - dplyr::filter(.data$rank == "all") -} - - - # Non exported functions ---------------------------------------------------- .makeSignaturesDiscrete <- function(dat, tax_id_type = "NCBI_ID") { dat |> @@ -216,22 +199,6 @@ importVal <- function() { ) |> {\(y) split(y, y$Attribute)}() |> lapply(function(x) unique(x[[tax_id_type]])) - # if (all(dat$Attribute_group != dat$Attribute)) { - # output <- dat |> - # dplyr::mutate( - # Attribute = paste0("bugphyzz:", .data$Attribute_group, "|", .data$Attribute, "|", .data$Attribute_value) - # ) |> - # {\(y) split(y, y$Attribute)}() |> - # lapply(function(x) unique(x[[tax_id_type]])) - # } else { - # output <- dat |> - # dplyr::mutate( - # Attribute = paste0("bugphyzz:", .data$Attribute, "|", .data$Attribute_value) - # ) |> - # {\(y) split(y, y$Attribute)}() |> - # lapply(function(x) unique(x[[tax_id_type]])) - # } - # return(output) } .makeSignaturesNumeric <- function( diff --git a/man/importVal.Rd b/man/importVal.Rd deleted file mode 100644 index 3cd17d50..00000000 --- a/man/importVal.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bugphyzz.R -\name{importVal} -\alias{importVal} -\title{Import validation data} -\usage{ -importVal() -} -\value{ -A data.frame. -} -\description{ -\code{importValidation} impots the result of the 10-fold cross-validation. -} -\examples{ - -val <- importValidation() - -}