Manual annotation don't work when labels are duplicated

[kassambara]

Hi,

As described in issue https://github.com/const-ae/ggsignif/issues/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))
  )
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

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: https://github.com/const-ae/ggsignif/issues/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?

[const-ae]

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

[kassambara]

Hi Constatin,

Thank you again for this awesome package.

I found a quick fix to my issue:

1. Adding group column: each row (i.e., comparison) is considered as a different group
2. Specifying the group in 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: https://github.com/const-ae/ggsignif/blob/4fbacff05ab349b4f10373b3b0bdbb4b70df5d7f/R/significance_annotation.R#L129)

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

[const-ae]

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.

[shiyun09]

I found a quick fix to my issue:

1. Adding group column: each row (i.e., comparison) is considered as a different group
2. Specifying the group in aes()

Hi, Alboukadel, great work. It solved my problem. Thank you !

[kassambara]

@shiyun09 you're welcome, I'm happy to know that it helps

[HannesOberreiter]

@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

[IndrajeetPatil]

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

``` r devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.3 (2020-10-10) #> os macOS Mojave 10.14.6 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Europe/Berlin #> date 2021-01-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib source #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) #> callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2) #> cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.3) #> colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.2) #> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) #> curl 4.3 2019-12-02 [1] CRAN (R 4.0.1) #> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) #> devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2) #> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2) #> dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2) #> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1) #> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) #> farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) #> generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2) #> ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.3) #> ggsignif * 0.6.0 2019-08-08 [1] CRAN (R 4.0.2) #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) #> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) #> highr 0.8 2019-03-20 [1] CRAN (R 4.0.2) #> htmltools 0.5.1 2021-01-12 [1] CRAN (R 4.0.3) #> httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) #> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2) #> labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.2) #> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3) #> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) #> mime 0.9 2020-02-04 [1] CRAN (R 4.0.2) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) #> pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.3) #> pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) #> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) #> processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.3) #> ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.3) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) #> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2) #> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) #> rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.3) #> rmarkdown 2.6 2020-12-14 [1] CRAN (R 4.0.3) #> rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3) #> scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) #> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) #> testthat 3.0.1 2020-12-17 [1] CRAN (R 4.0.3) #> tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.2) #> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) #> usethis 2.0.0 2020-12-10 [1] CRAN (R 4.0.3) #> vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.3) #> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2) #> xfun 0.20 2021-01-06 [1] CRAN (R 4.0.3) #> xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) #> #> [1] /Users/patil/Library/R/4.0/library #> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

[IndrajeetPatil]

Closing this as I can no longer reproduce this behavior. Please re-open it with a reprex if you can reproduce this issue again.

[mtcruz]

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

``` r devtools::session_info() #> - Session info --------------------------------------------------------------- #> setting value #> version R version 4.0.5 (2021-03-31) #> os Windows 10 x64 #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate Portuguese_Brazil.1252 #> ctype Portuguese_Brazil.1252 #> tz America/Sao_Paulo #> date 2021-11-09 #> #> - Packages ------------------------------------------------------------------- #> package * version date lib source #> cachem 1.0.4 2021-02-13 [1] CRAN (R 4.0.5) #> callr 3.6.0 2021-03-28 [1] CRAN (R 4.0.4) #> cli 2.4.0 2021-04-05 [1] CRAN (R 4.0.5) #> crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.5) #> desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.5) #> devtools 2.4.0 2021-04-07 [1] CRAN (R 4.0.5) #> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3) #> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.5) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3) #> highr 0.8 2019-03-20 [1] CRAN (R 4.0.2) #> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.5) #> knitr 1.31 2021-01-27 [1] CRAN (R 4.0.5) #> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.5) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3) #> memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.5) #> pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3) #> pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.5) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) #> processx 3.5.1 2021-04-04 [1] CRAN (R 4.0.5) #> ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.5) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) #> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3) #> remotes 2.3.0 2021-04-01 [1] CRAN (R 4.0.5) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.0.5) #> rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.5) #> rmarkdown 2.7 2021-02-19 [1] CRAN (R 4.0.5) #> rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) #> stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) #> testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.5) #> usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.5) #> withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.5) #> xfun 0.22 2021-03-11 [1] CRAN (R 4.0.5) #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) #> #> [1] C:/Users/mateu/Documents/R/win-library/4.0 #> [2] C:/Program Files/R/R-4.0.5/library ```

I 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.