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(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram

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dr. M.S. (Matthijs) Berends
2025-02-26 13:27:20 +01:00
parent b10989f431
commit 195dfb4b91
20 changed files with 107 additions and 42 deletions
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4
R/plotting.R
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@ -218,12 +218,10 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
}
scale$transform_df <- function(self, df) {
stop_if(all(is.na(df[[aest]])),
"`scale_", aest, "_mic()`: All MIC values are `NA`. Check your input data.", call = FALSE)
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
# create new breaks and labels here
lims <- range(self$mic_values_rescaled, na.rm = TRUE)
# support inner and outer mic_range settings (e.g., data ranges 0.5-8 and mic_range is set to 0.025-64)
# support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
if (!is.null(mic_range) && !is.na(mic_range[1]) && !is.na(lims[1]) && mic_range[1] < lims[1]) {
lims[1] <- mic_range[1]
}