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(v1.3.0.9038) prefinal 1.4.0

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dr. M.S. (Matthijs) Berends
2020-10-04 19:26:43 +02:00
parent 3136bc54aa
commit baf510183c
89 changed files with 570 additions and 548 deletions
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48
R/mo.R
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@ -157,7 +157,7 @@ as.mo <- function(x,
check_dataset_integrity()
if (tryCatch(all(x %in% MO_lookup$mo, na.rm = TRUE)
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# don't look into valid MO codes, just return them
@ -212,7 +212,7 @@ as.mo <- function(x,
pm_pull("mo")
)
} else if (all(x %in% MO_lookup$mo)
} else if (all(x[!is.na(x)] %in% MO_lookup$mo)
& isFALSE(Becker)
& isFALSE(Lancefield)) {
y <- x
@ -1733,7 +1733,9 @@ print.mo_uncertainties <- function(x, ...) {
if (NROW(x) == 0) {
return(NULL)
}
cat(font_blue(strwrap(c("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Please see ?mo_matching_score.")), collapse = "\n"))
cat(font_blue(strwrap("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Please see ?mo_matching_score.",
width = 0.98 * getOption("width")),
collapse = "\n"))
cat("\n")
msg <- ""
@ -1745,12 +1747,22 @@ print.mo_uncertainties <- function(x, ...) {
candidates <- candidates[order(1 - scores)]
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
n_candidates <- length(candidates)
candidates <- paste0(font_italic(candidates, collapse = NULL),
" (", scores_formatted[order(1 - scores)], ")")
candidates <- paste(candidates, collapse = ", ")
candidates <- paste0(candidates, " (", scores_formatted[order(1 - scores)], ")", collapse = ", ")
# align with input after arrow
candidates <- paste0("\n", strrep(" ", nchar(x[i, ]$input) + 6),
"Also matched", ifelse(n_candidates == 25, " (max 25)", ""), ": ", candidates)
candidates <- paste0("\n",
strwrap(paste0("Also matched",
ifelse(n_candidates >= 25, " (max 25)", ""), ": ",
candidates), # this is already max 25 due to format_uncertainty_as_df()
indent = nchar(x[i, ]$input) + 6,
exdent = nchar(x[i, ]$input) + 6,
width = 0.98 * getOption("width")),
collapse = "")
# after strwrap, make taxonomic names italic
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates)
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
"Also matched",
candidates, fixed = TRUE)
candidates <- gsub(font_italic("max"), "max", candidates, fixed = TRUE)
} else {
candidates <- ""
}
@ -1759,14 +1771,20 @@ print.mo_uncertainties <- function(x, ...) {
3),
format = "f", digits = 3))
msg <- paste(msg,
paste0('"', x[i, ]$input, '" -> ',
paste0(font_bold(font_italic(x[i, ]$fullname)),
ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
" (", x[i, ]$mo,
", matching score = ", score,
") "),
candidates),
paste0(
strwrap(
paste0('"', x[i, ]$input, '" -> ',
paste0(font_bold(font_italic(x[i, ]$fullname)),
ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
" (", x[i, ]$mo,
", matching score = ", score,
") ")),
width = 0.98 * getOption("width"),
exdent = nchar(x[i, ]$input) + 6),
collapse = "\n"),
candidates,
sep = "\n")
msg <- paste0(gsub("\n\n", "\n", msg), "\n\n")
}
cat(msg)
}