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Update geom_signif.R #133

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Update geom_signif.R #133

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d423fe3
Update geom_signif.R
elnaggarj Sep 4, 2023
c1ea713
FDR function description updated
elnaggarj Sep 4, 2023
57804be
Testing p value correction with facets
elnaggarj Sep 5, 2023
26150c4
debugging2
elnaggarj Sep 5, 2023
edd23c5
debugging 2
elnaggarj Sep 5, 2023
e7e428b
finished debuging
elnaggarj Sep 5, 2023
ad56df9
Changed FDR to correction
elnaggarj Sep 5, 2023
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8 changes: 8 additions & 0 deletions R/geom_signif.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@
#' annotations per facet.
#' @param na.rm If `FALSE` (the default), removes missing values with
#' a warning. If `TRUE` silently removes missing values.
#' @param correction Should the p value be corrected for multiple testing by false discovery rate ?
#' "none" by default. p.adjust.methods: c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
#' @param orientation The orientation of the layer. The default (‘NA’)
#' automatically determines the orientation from the aesthetic mapping.
#' In the rare event that this fails it can be given explicitly by setting
Expand Down Expand Up @@ -104,6 +106,7 @@ stat_signif <- function(mapping = NULL,
vjust = 0,
parse = FALSE,
manual = FALSE,
correction="none",
orientation = NA,
...) {
if (manual) {
Expand Down Expand Up @@ -137,6 +140,7 @@ stat_signif <- function(mapping = NULL,
parse = parse,
manual = manual,
na.rm = na.rm,
correction=correction,
orientation = orientation,
...
)
Expand Down Expand Up @@ -271,6 +275,7 @@ geom_signif <- function(mapping = NULL,
vjust = 0,
parse = FALSE,
manual = FALSE,
correction="none",
orientation = NA,
...) {
params <- list(na.rm = na.rm, ...)
Expand Down Expand Up @@ -327,6 +332,7 @@ geom_signif <- function(mapping = NULL,
vjust = vjust,
parse = parse,
manual = manual,
correction=correction,
orientation = orientation
)
)
Expand Down Expand Up @@ -427,6 +433,7 @@ StatSignif <- ggplot2::ggproto(
step_increase,
tip_length,
manual,
correction,
flipped_aes = FALSE) {
data <- ggplot2::flip_data(data, flipped_aes)
scales <- ggplot2::flip_data(scales, flipped_aes)
Expand Down Expand Up @@ -467,6 +474,7 @@ StatSignif <- ggplot2::ggproto(
group_2 <- complete_data$y[complete_data$x == scales$x$map(comp[2]) &
complete_data$PANEL == data$PANEL[1]]
p_value <- do.call(test, c(list(group_1, group_2), test.args))$p.value
p_value = p.adjust(p_value, method=correction, n=length(comparisons))
if (is.numeric(map_signif_level)) {
temp_value <- names(which.min(map_signif_level[which(map_signif_level > p_value)]))
if (is.null(temp_value)) {
Expand Down