Manual annotation don't work when labels are duplicated
kassambara opened this issue · 9 comments
Hi,
As described in issue #6, annotation that contain duplicate contents does not work for grouped plots.
Let's start by some reproducible examples.
Demo data and plot:
library(ggplot2)
library(ggsignif)
p <- ggplot(ToothGrowth, aes(supp, len)) +
geom_boxplot(aes(color = dose))
s <- stat.test <- data.frame(
stringsAsFactors=FALSE,
p.adj = c(0.000176, 3.96e-06, 0.0392, 1.36e-06, 1.4e-07, 9.16e-05),
signif = c("****", "****", "****", "****", "****", "****"),
signif2 = c("a", "b", "c", "d", "e", "f"),
y_position = c(31.827, 33.5295, 35.232, 34.917, 37.1445, 39.372),
xmin = c(0.7, 0.7, 1, 1.7, 1.7, 2),
xmax = c(1, 1.3, 1.3, 2, 2.3, 2.3),
group = rep(1:2, each = 3),
supp = as.factor(rep(c("OJ", "VC"), each = 3))
)
sp.adj signif signif2 y_position xmin xmax group supp 1 1.76e-04 **** a 31.8270 0.7 1.0 1 OJ 2 3.96e-06 **** b 33.5295 0.7 1.3 1 OJ 3 3.92e-02 **** c 35.2320 1.0 1.3 1 OJ 4 1.36e-06 **** d 34.9170 1.7 2.0 2 VC 5 1.40e-07 **** e 37.1445 1.7 2.3 2 VC 6 9.16e-05 **** f 39.3720 2.0 2.3 2 VC
Th following R code works because all annotation contents are distinct:
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif2),
data = stat.test, manual = TRUE, tip_length = 0
)
This one does not work because annotation contents are duplicated:
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif),
data = stat.test,
manual = TRUE, tip_length = 0
)
A workaround has been provided in discussion: #6
p + geom_signif(
xmin = s$xmin, xmax = s$xmax,
y_position = s$y_position, annotation = s$signif,
tip_length = 0
)
My problem is that, the above solution does not work when facet is used:
p + geom_signif(
xmin = s$xmin, xmax = s$xmax,
y_position = s$y_position, annotation = s$signif,
tip_length = 0
) +
facet_wrap(~supp)
Aesthetic mapping is better for faceting but annotations are not displayed correctly:
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif),
data = stat.test,
manual = TRUE, tip_length = 0
)+
facet_wrap(~supp)
Any suggestions?
Hi Alboukadel,
thank you for the excellent issue description and the reproducible example. Please execuse the delay, I am currently travelling (until the end of the month), and although I do have my laptop with me, I cannot promise that I will find time to look into the underlying problem and implement a fix.
But, i would be very happy to accept a pull request. From your repos, I have the impression that you have the necessary experience with ggplot extensions ;)
Best, Constantin
Hi Constatin,
Thank you again for this awesome package.
I found a quick fix to my issue:
- Adding group column: each row (i.e., comparison) is considered as a different group
- Specifying the
groupin aes()
stat.test$group <- 1:nrow(stat.test)
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif, group = group),
data = stat.test, manual = TRUE, tip_length = 0, vjust = 0.5
)
From my point of view, when manual = TRUE, then each annotation can be automatically considered as a different group.
If you think that it's a good user-experience to have this grouping done automatically, then the function geom_signif() can be simply modified as follow:
Replacing :
group=if(manual){rep(data$group, times=3)} (in line:
ggsignif/R/significance_annotation.R
Line 129 in 4fbacff
by:
group=if(manual){rep(1:xmin, times=3)}
If this modification is not necessary, then we can close this issue
Have a good trip!
Alboukadel
Thank you again for this awesome package.
Well, thank you for most its downloads :)
I found a quick fix to my issue
That's great to hear. And for your suggestion, I will have to have a more thorough look, so I will leave the issue open and take another look when I am back.
Have a good trip!
Thanks.
I found a quick fix to my issue:
- Adding group column: each row (i.e., comparison) is considered as a different group
- Specifying the
groupin aes()
Hi, Alboukadel, great work. It solved my problem. Thank you !
@shiyun09 you're welcome, I'm happy to know that it helps
@kassambara thank you, I run in this problem and your workaround was exactly what I needed.
I use rstatix and add manually the signf. values and it did not work when the annotations were the same. Now I use simply the p.adj column as a dummy group.
custom_p <- DATA %>% rstatix::dunn_test(costs ~ 0 + tri_size, p.adjust.method = "holm")
custom_p <- pwc %>% rstatix::add_xy_position(x = "tri_size")
ggplot(data, aes()) + geom_boxplot() + ...
ggsignif::geom_signif(
data=custom_p,
aes(xmin = xmin, xmax = xmax, annotations = p.adj.signif, y_position = y.position, group = p.adj),
manual=TRUE)With group:
Without group:
Cheers
Hannes
I am revisiting this, but I can't actually reproduce the original behavior. I am not sure if this has something to do with ggplot2 itself having changed:
library(ggplot2)
library(ggsignif)
p <- ggplot(ToothGrowth, aes(supp, len)) +
geom_boxplot(aes(color = dose))
s <- stat.test <- data.frame(
stringsAsFactors=FALSE,
p.adj = c(0.000176, 3.96e-06, 0.0392, 1.36e-06, 1.4e-07, 9.16e-05),
signif = c("****", "****", "****", "****", "****", "****"),
signif2 = c("a", "b", "c", "d", "e", "f"),
y_position = c(31.827, 33.5295, 35.232, 34.917, 37.1445, 39.372),
xmin = c(0.7, 0.7, 1, 1.7, 1.7, 2),
xmax = c(1, 1.3, 1.3, 2, 2.3, 2.3),
group = rep(1:2, each = 3),
supp = as.factor(rep(c("OJ", "VC"), each = 3))
)
s
#> p.adj signif signif2 y_position xmin xmax group supp
#> 1 1.76e-04 **** a 31.8270 0.7 1.0 1 OJ
#> 2 3.96e-06 **** b 33.5295 0.7 1.3 1 OJ
#> 3 3.92e-02 **** c 35.2320 1.0 1.3 1 OJ
#> 4 1.36e-06 **** d 34.9170 1.7 2.0 2 VC
#> 5 1.40e-07 **** e 37.1445 1.7 2.3 2 VC
#> 6 9.16e-05 **** f 39.3720 2.0 2.3 2 VC
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif2),
data = stat.test, manual = TRUE, tip_length = 0
)
#> Warning: Ignoring unknown aesthetics: xmin, xmax, y_position, annotations
Created on 2021-01-13 by the reprex package (v0.3.0)
Session info
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#> [1] /Users/patil/Library/R/4.0/library
#> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/libraryClosing this as I can no longer reproduce this behavior. Please re-open it with a reprex if you can reproduce this issue again.
I found a way of replicating the original reprex. The variable "dose" from "ToothGrowth" needs to be a factor to enable the color mapping. I suppose the OP (@kassambara) changed "ToothGrowth" before posting.
library(ggplot2)
library(ggsignif)
p <- ggplot(ToothGrowth, aes(supp, len)) +
geom_boxplot(aes(color = as.factor(dose)))
s <- stat.test <- data.frame(
stringsAsFactors=FALSE,
p.adj = c(0.000176, 3.96e-06, 0.0392, 1.36e-06, 1.4e-07, 9.16e-05),
signif = c("****", "****", "****", "****", "****", "****"),
signif2 = c("a", "b", "c", "d", "e", "f"),
y_position = c(31.827, 33.5295, 35.232, 34.917, 37.1445, 39.372),
xmin = c(0.7, 0.7, 1, 1.7, 1.7, 2),
xmax = c(1, 1.3, 1.3, 2, 2.3, 2.3),
group = rep(1:2, each = 3),
supp = as.factor(rep(c("OJ", "VC"), each = 3))
)
p + geom_signif(
aes(xmin = xmin, xmax = xmax, y_position = y_position, annotations = signif),
data = stat.test,
manual = TRUE, tip_length = 0
)
#> Warning: Ignoring unknown aesthetics: xmin, xmax, y_position, annotations
Created on 2021-11-09 by the reprex package (v2.0.1)
Session Info
devtools::session_info()
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#>
#> [1] C:/Users/mateu/Documents/R/win-library/4.0
#> [2] C:/Program Files/R/R-4.0.5/libraryI agree with Alboukadel when he says that
it's a good user-experience to have this grouping done automatically
I hope to see this added/fixed soon!
Best,
Mateus.