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(v3.0.0.9014) fix plot colours

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dr. M.S. (Matthijs) Berends
2025-07-18 15:57:48 +02:00
parent 8da0f525b5
commit 49274f010b
7 changed files with 91 additions and 64 deletions
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index.md
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@ -171,14 +171,14 @@ example_isolates %>%
select(bacteria,
aminoglycosides(),
carbapenems())
#> ℹ Using column 'mo' as input for mo_fullname()
#> ℹ Using column 'mo' as input for mo_is_gram_negative()
#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
#> ℹ Using column 'mo' as input for `mo_fullname()`
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@ -215,9 +215,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()))
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@ -289,7 +289,7 @@ ggplot(data.frame(mic = some_mic_values,
sir = interpretation),
aes(x = group, y = mic, colour = sir)) +
theme_minimal() +
geom_boxplot(fill = NA, colour = "grey") +
geom_boxplot(fill = NA, colour = "grey30") +
geom_jitter(width = 0.25) +
# NEW scale function: plot MIC values to x, y, colour or fill
@ -340,15 +340,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For polymyxins() using column 'COL' (colistin)
#> ℹ For `polymyxins()` using column 'COL' (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (minimum = 30).
#> "Outpatient" (`minimum` = 30).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL