P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 05:41:59 +02:00
Code Releases Activity

(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-26 17:19:17 +01:00
parent 8deaf2c8eb
commit e6f88241b2
53 changed files with 552 additions and 334 deletions
Download Patch File Download Diff File Expand all files Collapse all files

58
R/plotting.R
View File

@ -243,31 +243,47 @@ 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$transform_df <- function(self, df) {
self$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$mic_values_rescaled, na.rm = TRUE)
# support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
if (!is.null(mic_range) && !is.na(mic_range[1]) && !is.na(lims[1]) && mic_range[1] < lims[1]) {
lims[1] <- mic_range[1]
}
if (!is.null(mic_range) && !is.na(mic_range[2]) && !is.na(lims[2]) && mic_range[2] > lims[2]) {
lims[2] <- mic_range[2]
}
ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))] # Closest index where COMMON_MIC_VALUES <= lims[1]
ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
if (!aest %in% colnames(df)) {
# support for geom_hline() and geom_vline()
if ("yintercept" %in% colnames(df)) {
aest_val <- "yintercept"
} else if ("xintercept" %in% colnames(df)) {
aest_val <- "xintercept"
} else {
stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
}
out <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
if (!is.null(self$mic_values_rescaled) && any(out < min(self$mic_values_rescaled, na.rm = TRUE) | out > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
}
df[[aest_val]] <- log2(as.double(out))
} else {
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., 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]
}
if (!is.null(mic_range) && !is.na(mic_range[2]) && !is.na(lims[2]) && mic_range[2] > lims[2]) {
lims[2] <- mic_range[2]
}
ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))] # Closest index where COMMON_MIC_VALUES <= lims[1]
ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
if (keep_operators %in% c("edges", "all") && length(self$mic_values_levels) > 1) {
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
}
if (keep_operators %in% c("edges", "all") && length(unique(self$mic_values_levels)) > 1) {
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
}
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df)) {
df$group <- as.integer(factor(df$x))
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
df$group <- as.integer(factor(df$x))
}
df[[aest]] <- self$mic_values_log
}
df[[aest]] <- self$mic_values_log
df
}