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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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9 changes: 9 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 +39,7 @@
#' annotations per facet.
#' @param na.rm If `FALSE` (the default), removes missing values with
#' a warning. If `TRUE` silently removes missing values.
#' @param FDR logical. Should the p value be corrected for multiple testing by false discovery rate ? FALSE by default.
#' @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 +105,7 @@ stat_signif <- function(mapping = NULL,
vjust = 0,
parse = FALSE,
manual = FALSE,
FDR=FALSE,
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orientation = NA,
...) {
if (manual) {
Expand Down Expand Up @@ -137,6 +139,7 @@ stat_signif <- function(mapping = NULL,
parse = parse,
manual = manual,
na.rm = na.rm,
FDR=FDR,
orientation = orientation,
...
)
Expand Down Expand Up @@ -271,6 +274,7 @@ geom_signif <- function(mapping = NULL,
vjust = 0,
parse = FALSE,
manual = FALSE,
FDR=FALSE,
orientation = NA,
...) {
params <- list(na.rm = na.rm, ...)
Expand Down Expand Up @@ -327,6 +331,7 @@ geom_signif <- function(mapping = NULL,
vjust = vjust,
parse = parse,
manual = manual,
FDR=FDR,
orientation = orientation
)
)
Expand Down Expand Up @@ -427,6 +432,7 @@ StatSignif <- ggplot2::ggproto(
step_increase,
tip_length,
manual,
FDR,
flipped_aes = FALSE) {
data <- ggplot2::flip_data(data, flipped_aes)
scales <- ggplot2::flip_data(scales, flipped_aes)
Expand Down Expand Up @@ -467,6 +473,9 @@ 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
if(FDR==TRUE){
p_value = p.adjust(p_value, method="fdr", 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