The solution given above by @dww (use label = "p.signif") is the correct one:
cmpr
myplot + stat_compare_means(comparisons = cmpr, tip.length=0.01,
label = "p.signif",
symnum.args = list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1),
symbols = c("****", "***", "**", "*", "ns")))
EDIT: I modified stat_compare_means because this function seems to ignore symnum.args:
my_stat_compare_means
method.args = list(), ref.group = NULL, comparisons = NULL,
hide.ns = FALSE, label.sep = ", ", label = NULL, label.x.npc = "left",
label.y.npc = "top", label.x = NULL, label.y = NULL, tip.length = 0.03,
symnum.args = list(), geom = "text", position = "identity",
na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
{
if (!is.null(comparisons)) {
method.info
method
method.args
if (method == "wilcox.test")
method.args$exact
pms
size
color
map_signif_level
if (is.null(label))
label
if (ggpubr:::.is_p.signif_in_mapping(mapping) | (label %in% "p.signif")) {
if (ggpubr:::.is_empty(symnum.args)) {
map_signif_level
`**` = 0.01, `*` = 0.05, ns = 1)
} else {
map_signif_level
}
if (hide.ns)
names(map_signif_level)[5]
}
step_increase
ggsignif::geom_signif(comparisons = comparisons, y_position = label.y,
test = method, test.args = method.args, step_increase = step_increase,
size = size, color = color, map_signif_level = map_signif_level,
tip_length = tip.length, data = data)
} else {
mapping
layer(stat = StatCompareMeans, data = data, mapping = mapping,
geom = geom, position = position, show.legend = show.legend,
inherit.aes = inherit.aes, params = list(label.x.npc = label.x.npc,
label.y.npc = label.y.npc, label.x = label.x,
label.y = label.y, label.sep = label.sep, method = method,
method.args = method.args, paired = paired, ref.group = ref.group,
symnum.args = symnum.args, hide.ns = hide.ns,
na.rm = na.rm, ...))
}
}
symnum.args
myplot + my_stat_compare_means(comparisons = cmpr, tip.length=0.01,
label = "p.signif", symnum.args = symnum.args)