mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 07:26:13 +01:00
216 lines
8.4 KiB
R
216 lines
8.4 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
# print successful as.mo coercions to a options entry
|
|
#' @importFrom dplyr %>% distinct filter
|
|
#' @importFrom utils write.csv
|
|
set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {
|
|
if (isTRUE(disable)) {
|
|
return(base::invisible())
|
|
}
|
|
|
|
# don't save codes that are in a code data set already
|
|
mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
|
|
x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
|
|
|
|
warning_new_write <- FALSE
|
|
|
|
if (base::interactive() | force == TRUE) {
|
|
mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
|
|
df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
|
|
distinct(x, .keep_all = TRUE) %>%
|
|
filter(!is.na(x) & !is.na(mo))
|
|
if (nrow(df) == 0) {
|
|
return(base::invisible())
|
|
}
|
|
x <- toupper(df$x)
|
|
mo <- df$mo
|
|
for (i in 1:length(x)) {
|
|
# save package version too, as both the as.mo() algorithm and the reference data set may change
|
|
if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
|
|
mo_hist$uncertainty_level >= uncertainty_level &
|
|
mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
|
|
# # Not using the file system:
|
|
# tryCatch(options(mo_remembered_results = rbind(mo_hist,
|
|
# data.frame(
|
|
# x = x[i],
|
|
# mo = mo[i],
|
|
# uncertainty_level = uncertainty_level,
|
|
# package_version = base::as.character(utils::packageVersion("AMR")),
|
|
# stringsAsFactors = FALSE))),
|
|
# error = function(e) base::invisible())
|
|
# # don't remember more than 1,000 different input values
|
|
# if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
|
|
# return(base::invisible())
|
|
# }
|
|
if (is.null(mo_hist) & interactive()) {
|
|
warning_new_write <- TRUE
|
|
}
|
|
tryCatch(write.csv(rbind(mo_hist,
|
|
data.frame(
|
|
x = x[i],
|
|
mo = mo[i],
|
|
uncertainty_level = uncertainty_level,
|
|
package_version = base::as.character(utils::packageVersion("AMR")),
|
|
stringsAsFactors = FALSE)),
|
|
row.names = FALSE,
|
|
file = mo_history_file()),
|
|
error = function(e) { warning_new_write <- FALSE; base::invisible()})
|
|
}
|
|
}
|
|
}
|
|
if (warning_new_write == TRUE) {
|
|
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
|
|
}
|
|
return(base::invisible())
|
|
}
|
|
|
|
get_mo_history <- function(x, uncertainty_level, force = FALSE, disable = FALSE) {
|
|
if (isTRUE(disable)) {
|
|
return(to_class_mo(NA))
|
|
}
|
|
|
|
history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
|
|
if (base::is.null(history)) {
|
|
result <- NA
|
|
} else {
|
|
result <- data.frame(x = as.character(toupper(x)), stringsAsFactors = FALSE) %>%
|
|
left_join(history, by = "x") %>%
|
|
pull(mo)
|
|
}
|
|
to_class_mo(result)
|
|
}
|
|
|
|
#' @importFrom dplyr %>% filter distinct
|
|
#' @importFrom utils read.csv
|
|
read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE, disable = FALSE) {
|
|
if (isTRUE(disable)) {
|
|
return(NULL)
|
|
}
|
|
|
|
if ((!base::interactive() & force == FALSE)) {
|
|
return(NULL)
|
|
}
|
|
uncertainty_level_param <- uncertainty_level
|
|
|
|
# # Not using the file system:
|
|
# history <- tryCatch(getOption("mo_remembered_results"),
|
|
# error = function(e) NULL)
|
|
history <- tryCatch(read.csv(mo_history_file(), stringsAsFactors = FALSE),
|
|
warning = function(w) invisible(),
|
|
error = function(e) NULL)
|
|
if (is.null(history)) {
|
|
return(NULL)
|
|
}
|
|
# Below: filter on current package version.
|
|
# Even current fullnames may be replaced by new taxonomic names, so new versions of
|
|
# the Catalogue of Life must not lead to data corruption.
|
|
|
|
if (unfiltered == FALSE) {
|
|
history <- history %>%
|
|
filter(package_version == as.character(utils::packageVersion("AMR")),
|
|
# only take unknowns if uncertainty_level_param is higher
|
|
((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
|
|
(mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
|
|
arrange(desc(uncertainty_level)) %>%
|
|
distinct(x, mo, .keep_all = TRUE)
|
|
}
|
|
|
|
if (nrow(history) == 0) {
|
|
NULL
|
|
} else {
|
|
history
|
|
}
|
|
}
|
|
|
|
#' @rdname as.mo
|
|
#' @importFrom crayon red
|
|
#' @importFrom utils menu
|
|
#' @export
|
|
clear_mo_history <- function(...) {
|
|
if (!is.null(read_mo_history())) {
|
|
if (interactive() & !isTRUE(list(...)$force)) {
|
|
q <- menu(title = paste("This will clear all",
|
|
format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
|
|
"previously determined microbial IDs. Are you sure?"),
|
|
choices = c("Yes", "No"),
|
|
graphics = FALSE)
|
|
if (q != 1) {
|
|
return(invisible())
|
|
}
|
|
}
|
|
# # Not using the file system:
|
|
# success <- tryCatch(options(mo_remembered_results = NULL),
|
|
# error = function(e) FALSE)
|
|
success <- create_blank_mo_history()
|
|
if (!isFALSE(success)) {
|
|
cat(red(paste("File", mo_history_file(), "cleared.")))
|
|
}
|
|
}
|
|
}
|
|
|
|
#' @importFrom utils write.csv
|
|
create_blank_mo_history <- function() {
|
|
tryCatch(
|
|
write.csv(x = data.frame(x = character(0),
|
|
mo = character(0),
|
|
uncertainty_level = integer(0),
|
|
package_version = character(0),
|
|
stringsAsFactors = FALSE),
|
|
row.names = FALSE,
|
|
file = mo_history_file()),
|
|
warning = function(w) invisible(),
|
|
error = function(e) TRUE)
|
|
}
|
|
|
|
|
|
# Borrowed all below code from the extrafont package,
|
|
# https://github.com/wch/extrafont/blob/254c3f99b02f11adb59affbda699a92aec8624f5/R/utils.r
|
|
inst_path <- function() {
|
|
envname <- environmentName(parent.env(environment()))
|
|
|
|
# If installed in package, envname == "AMR"
|
|
# If loaded with load_all, envname == "package:AMR"
|
|
# (This is kind of strange)
|
|
if (envname == "AMR") {
|
|
system.file(package = "AMR")
|
|
} else {
|
|
srcfile <- attr(attr(inst_path, "srcref"), "srcfile")
|
|
file.path(dirname(dirname(srcfile$filename)), "inst")
|
|
}
|
|
}
|
|
|
|
|
|
# Get the path where extrafontdb is installed
|
|
db_path <- function() {
|
|
system.file(package = "AMR")
|
|
}
|
|
|
|
# fonttable file
|
|
mo_history_file <- function() {
|
|
file.path(mo_history_path(), "mo_history.csv")
|
|
}
|
|
|
|
# Path of fontmap directory
|
|
mo_history_path <- function() {
|
|
file.path(db_path(), "mo_history")
|
|
}
|