mirror of https://github.com/msberends/AMR.git
118 lines
5.0 KiB
R
118 lines
5.0 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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# print successful as.mo coercions to file, not uncertain ones
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#' @importFrom dplyr %>% distinct filter
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set_mo_history <- function(x, mo, uncertainty_level, force = FALSE) {
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file_location <- base::path.expand('~/.Rhistory_mo')
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if (base::interactive() | force == TRUE) {
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mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
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distinct(x, .keep_all = TRUE) %>%
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filter(!is.na(x) & !is.na(mo))
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if (nrow(df) == 0) {
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return(base::invisible())
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}
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x <- toupper(df$x)
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mo <- df$mo
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for (i in 1:length(x)) {
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# save package version too, as both the as.mo() algorithm and the reference data set may change
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if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
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mo_hist$uncertainty_level >= uncertainty_level &
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mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
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base::write(x = c(x[i], mo[i], uncertainty_level, base::as.character(utils::packageVersion("AMR"))),
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file = file_location,
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ncolumns = 4,
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append = TRUE,
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sep = "\t")
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}
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}
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}
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return(base::invisible())
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}
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get_mo_history <- function(x, uncertainty_level, force = FALSE) {
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file_read <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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if (base::is.null(file_read)) {
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NA
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} else {
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data.frame(x = toupper(x), stringsAsFactors = FALSE) %>%
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left_join(file_read, by = "x") %>%
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pull(mo)
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}
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}
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#' @importFrom dplyr %>% filter distinct
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read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE) {
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file_location <- base::path.expand('~/.Rhistory_mo')
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if (!base::file.exists(file_location) | (!base::interactive() & force == FALSE)) {
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return(NULL)
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}
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uncertainty_level_param <- uncertainty_level
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file_read <- utils::read.table(file = file_location,
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header = FALSE,
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sep = "\t",
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col.names = c("x", "mo", "uncertainty_level", "package_version"),
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stringsAsFactors = FALSE)
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# Below: filter on current package version.
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# Even current fullnames may be replaced by new taxonomic names, so new versions of
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# the Catalogue of Life must not lead to data corruption.
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if (unfiltered == FALSE) {
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file_read <- file_read %>%
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filter(package_version == utils::packageVersion("AMR"),
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# only take unknowns if uncertainty_level_param is higher
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((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
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(mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
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arrange(desc(uncertainty_level)) %>%
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distinct(x, mo, .keep_all = TRUE)
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}
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if (nrow(file_read) == 0) {
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NULL
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} else {
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file_read
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}
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}
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#' @rdname as.mo
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#' @importFrom crayon red
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#' @importFrom utils menu
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#' @export
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clean_mo_history <- function(...) {
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file_location <- base::path.expand('~/.Rhistory_mo')
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if (file.exists(file_location)) {
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if (interactive() & !isTRUE(list(...)$force)) {
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q <- menu(title = paste("This will remove all",
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format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
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"previously determined microbial IDs. Are you sure?"),
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choices = c("Yes", "No"),
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graphics = FALSE)
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if (q != 1) {
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return(invisible())
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}
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}
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unlink(file_location)
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cat(red("File", file_location, "removed."))
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}
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}
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