Perform manual annotations with ggsignif - r

Question

I am hoping to add manual comparisons and annotations to a ggplot with facets. While the previous stack overflow questions have been helpful, transitioning to multiple pairwise comparison per facet has been tricky.
Fortunately, the authors give a great section on this at the bottom of https://github.com/const-ae/ggsignif titled "Advanced Example". It has been modified to show it's possible to add multiple pairwise comparison in one facet box:
library(ggplot2)
library(ggsignif)
annotation_df <- data.frame(
color = c("E", "E"),
start = c("Good", "Fair"),
end = c("Fair", "Very Good"),
y = c(3.6, 4.7),
label = c("Comp. 1", "Comp. 2")
)
ggplot(diamonds, aes(x = cut, y = carat)) +
geom_boxplot() +
geom_signif(
data = annotation_df,
aes(xmin = start, xmax = end, annotations = label, y_position = y),
textsize = 3, vjust = -0.2,
manual = TRUE
) +
facet_wrap(~color) +
ylim(NA, 5.3)
Great, but when I do something similar, I seem only able to get one number produced. Additionally, I can't get it to graph without fill being set. What might be causing this issue?
library(ggplot2)
library(ggsignif)
library(dplyr)
EnrichmentDF <- data.frame(
cancer = c(rep("BRCA", 3), rep("PRAD", 3), rep("PAAD", 3)),
occurance = c(166, 152, 90, 288, 512, 291, 58, 145, 101),
cluster = rep(1:3)
)
Cancer <- apply(EnrichmentDF, 1, function(x)rep(x[1], x[2])) %>% unlist()
Cluster <- apply(EnrichmentDF, 1, function(x)rep(x[3], x[2])) %>% unlist()
niceTable <- table(Cancer, Cluster)
EnrichmentDF <- as.data.frame(niceTable)
colnames(EnrichmentDF) <- c("Cancer", "Cluster", "NumberOfPatients")
EnrichmentDF$CancerTotalN <- rowSums(niceTable)
EnrichmentDF$Percentage <- round(100 * EnrichmentDF$NumberOfPatients / EnrichmentDF$CancerTotalN, 2)
SignificanceStorage <- runif(9, 0.001, 0.2)
SignificanceDF <- data.frame(Cancer = rep(unique(EnrichmentDF$Cancer), each = ncol(niceTable)),
start = c(1,1,2), end = c(2, 3, 3),
y = c(75, 95, 125),
label = signif(SignificanceStorage, digits=2)
)
EnrichmentDF %>% ggplot(aes(x = Cluster, y= Percentage, fill = Cancer)) + # example did not have fill but breaks without it
geom_bar(aes(fill = Cluster), stat = "identity",
position = "dodge", width = .5) +
geom_signif(
data = SignificanceDF,
aes(xmin = start, xmax = end, annotations = label, y_position = y),
textsize = 3, vjust = -0.2,
manual = TRUE) +
facet_wrap(~Cancer) + ylim(0, 130) +
theme_bw()
This question is similar to this question, but without depreciation fixes leading to consistent overlaps

Answer 1

Thanks to TarJae and the contributors to the post here: https://github.com/const-ae/ggsignif/issues/63, an issue has been found requiring a group = in the parameters of geom_signif when faceting. While the comment on github mentions it's due to duplicated data, I do not see such in the example provided here.
These are the changes:
SignificanceDF$group <- 1:nrow(SignificanceDF)
EnrichmentDF %>% ggplot(aes(x = Cluster, y= Percentage)) +
and have been marked by a double ##
library(ggplot2)
library(ggsignif)
library(dplyr)
EnrichmentDF <- data.frame(
cancer = c(rep("BRCA", 3), rep("PRAD", 3), rep("PAAD", 3)),
occurance = c(166, 152, 90, 288, 512, 291, 58, 145, 101),
cluster = rep(1:3)
)
Cancer <- apply(EnrichmentDF, 1, function(x)rep(x[1], x[2])) %>% unlist()
Cluster <- apply(EnrichmentDF, 1, function(x)rep(x[3], x[2])) %>% unlist()
niceTable <- table(Cancer, Cluster)
EnrichmentDF <- as.data.frame(niceTable)
colnames(EnrichmentDF) <- c("Cancer", "Cluster", "NumberOfPatients")
EnrichmentDF$CancerTotalN <- rowSums(niceTable)
EnrichmentDF$Percentage <- round(100 * EnrichmentDF$NumberOfPatients / EnrichmentDF$CancerTotalN, 2)
SignificanceStorage <- runif(9, 0.001, 0.2)
SignificanceDF <- data.frame(Cancer = rep(unique(EnrichmentDF$Cancer), each = ncol(niceTable)),
start = c(1,1,2), end = c(2, 3, 3),
y = c(75, 95, 125),
label = signif(SignificanceStorage, digits=2)
)
SignificanceDF$group <- 1:nrow(SignificanceDF) ## NEW CODE ADDED
EnrichmentDF %>% ggplot(aes(x = Cluster, y= Percentage)) + ## REMOVED FILL
geom_bar(aes(fill = Cluster), stat = "identity",
position = "dodge", width = .5) +
geom_signif(
data = SignificanceDF,
aes(xmin = start, xmax = end, annotations = label, y_position = y),
textsize = 3, vjust = -0.2,
manual = TRUE) +
facet_wrap(~Cancer) + ylim(0, 130) +
theme_bw()