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(v3.0.1.9040) fix MIC plotting

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dr. M.S. (Matthijs) Berends
2026-03-24 12:44:47 +01:00
parent 2a8a1eda97
commit 9c95aa455c
10 changed files with 69 additions and 36 deletions
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10
R/mo.R
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@@ -648,13 +648,13 @@ pillar_shaft.mo <- function(x, ...) {
add_MO_lookup_to_AMR_env()
out <- trimws(format(x))
# grey out the kingdom (part until first "_")
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(pillar::style_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
# and grey out every _
out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
out[!is.na(x)] <- gsub("_", pillar::style_subtle("_"), out[!is.na(x)])
# markup NA and UNKNOWN
out[is.na(x)] <- font_na(" NA")
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
out[is.na(x)] <- pillar::style_na(" NA")
out[x == "UNKNOWN"] <- pillar::style_na(" UNKNOWN")
# markup manual codes
out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo] <- font_blue(out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo], collapse = NULL)
@@ -673,7 +673,7 @@ pillar_shaft.mo <- function(x, ...) {
(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
# markup old mo codes
out[!x %in% all_mos] <- font_italic(
font_na(x[!x %in% all_mos],
pillar::style_na(x[!x %in% all_mos],
collapse = NULL
),
collapse = NULL