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update gheatmap to be compatible with ggplot2-4.0.0 #668

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Oct 16, 2025
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update gheatmap to be compatible with ggplot2-4.0.0 #668

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32 changes: 16 additions & 16 deletions R/gheatmap.R
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Original file line number Diff line number Diff line change
Expand Up @@ -104,8 +104,8 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
dd$variable <- factor(dd$variable, levels=colnames_level)
}
V2 <- start + as.numeric(dd$variable) * width
mapping <- data.frame(from=dd$variable, to=V2)
mapping <- unique(mapping)
data_axis <- data.frame(from=dd$variable, to=V2)
data_axis <- unique(data_axis)

dd$x <- V2
dd$width <- width
Expand All @@ -127,25 +127,25 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
} else {
y <- max(p$data$y) + 1
}
mapping$y <- y
mapping[[".panel"]] <- factor("Tree")
data_axis$y <- y
data_axis[[".panel"]] <- factor("Tree")
# if custom column annotations are provided
if (!is.null(custom_column_labels)) {
# assess the type of input for the custom column annotation
# either a vector or a named vector with positions for specific names
if (is.null(names(custom_column_labels))) {
if (length(custom_column_labels) > nrow(mapping)) {
if (length(custom_column_labels) > nrow(data_axis)) {
warning(paste("Input column label vector has more elements than there are columns.",
"\n", "Using the first ", nrow(mapping)," elements as labels", sep=""))
mapping[["custom_labels"]] <- as.character(custom_column_labels[1:nrow(mapping)])
} else if (length(custom_column_labels) < nrow(mapping)) {
"\n", "Using the first ", nrow(data_axis)," elements as labels", sep=""))
data_axis[["custom_labels"]] <- as.character(custom_column_labels[1:nrow(data_axis)])
} else if (length(custom_column_labels) < nrow(data_axis)) {
warning(paste("Input column label vector has fewer elements than there are columns.",
"\n", "Using all available labels, n = ",
length(custom_column_labels), sep=""))
mapping[["custom_labels"]] <- as.character(c(custom_column_labels,
rep("", nrow(mapping) - length(custom_column_labels))))
data_axis[["custom_labels"]] <- as.character(c(custom_column_labels,
rep("", nrow(data_axis) - length(custom_column_labels))))
} else {
mapping[["custom_labels"]] <- custom_column_labels
data_axis[["custom_labels"]] <- custom_column_labels
}
} else {
if (!is.null(colnames_level)) {
Expand All @@ -154,18 +154,18 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
vector_order <- colnames_level

} else {
vector_order <- as.character(mapping$from)
vector_order <- as.character(data_axis$from)
}
for (elem in custom_column_labels) {
vector_order[which(vector_order == elem)] = names(which(custom_column_labels == elem))
}
mapping[["custom_labels"]] <- vector_order
data_axis[["custom_labels"]] <- vector_order
}
p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=custom_labels),
p2 <- p2 + geom_text(data=data_axis, aes(x=to, y = y, label=custom_labels),
size=font.size, family=family, inherit.aes = FALSE, angle=colnames_angle,
nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
} else {
p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), size=font.size, family=family,
p2 <- p2 + geom_text(data=data_axis, aes(x=to, y = y, label=from), size=font.size, family=family,
inherit.aes = FALSE, angle=colnames_angle,
nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
}
Expand All @@ -178,7 +178,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
p2 <- p2 + scale_y_continuous(expand = c(0,0))
}

attr(p2, "mapping") <- mapping
attr(p2, "data_axis") <- data_axis
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Is this needed; is this even evaluated in ggplot? Can this line be just removed?

return(p2)
}