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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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39
R/plotting.R
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@@ -266,7 +266,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
}
out[[aest_val]] <- log2(as.double(mics))
} else {
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
self$mic_values_rescaled <- rescale_mic(x = as.character(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
# create new breaks and labels here
lims <- range(self$mic_values_rescaled, na.rm = TRUE)
# support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
@@ -280,11 +280,21 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
if (length(unique(self$mic_values_levels)) > 1) {
if (keep_operators == "all" && !all(self$mic_values_rescaled %in% self$mic_values_levels, na.rm = TRUE)) {
self$mic_values_levels <- unique(sort(c(self$mic_values_levels, self$mic_values_rescaled)))
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$mic_values_levels)])
# collision = same log2 position, but different string labels
log_positions <- log2(as.double(self$mic_values_levels))
dup_positions <- log_positions[duplicated(log_positions) | duplicated(log_positions, fromLast = TRUE)]
colliding_labels <- as.character(self$mic_values_levels)[log_positions %in% dup_positions]
self$warn_keep_all_operators <- length(unique(colliding_labels)) > 1
} else if (keep_operators == "edges") {
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)) {
@@ -312,7 +322,26 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
}
scale$labels <- function(..., self) {
if (is.null(self$mic_breaks_set)) {
self$mic_values_levels
if (isTRUE(self$warn_keep_all_operators)) {
lookup <- tapply(
as.character(self$mic_values_rescaled),
self$mic_values_log,
function(x) paste(unique(x), collapse = ", ")
)
level_log <- as.character(log2(as.double(self$mic_values_levels)))
if (any(grepl(", ", lookup))) {
warning_("Using {.arg keep_operators = \"all\"} caused MIC values with different operators to share the same log2 position on the axis. These have been combined into a single label (e.g., {.val ", lookup[grepl(", ", lookup)][1], "}).", call = FALSE)
}
ifelse(
level_log %in% names(lookup),
lookup[level_log],
as.character(self$mic_values_levels)
)
} else {
self$mic_values_levels
}
} else {
breaks <- tryCatch(scale$breaks(), error = function(e) NULL)
if (!is.null(breaks)) {