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Manual annotation don't work when labels are duplicated #63

Open
kassambara opened this issue Jun 6, 2019 · 9 comments
Open

Manual annotation don't work when labels are duplicated #63

kassambara opened this issue Jun 6, 2019 · 9 comments
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reprex

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@kassambara
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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))
  )
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
    )

Rplot05

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
    )

Rplot06

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
)

Rplot07

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)

Rplot08

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)

Rplot09

Any suggestions?
@const-ae
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Owner

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
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Author

kassambara commented Jun 11, 2019 •
edited
Loading

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
)

Rplot10

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

annotation=rep(annotations, times=3), group=if(manual){rep(data$group, times=3)}else{rep(seq_along(xmin), times=3)})
)

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
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Owner

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
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shiyun09 commented Jun 27, 2020 •
edited
Loading

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
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Author

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

@HannesOberreiter
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@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:

with group

Without group:

without group

Cheers
Hannes

@muhark muhark mentioned this issue Dec 10, 2020
Open
@IndrajeetPatil
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IndrajeetPatil commented Jan 13, 2021 •
edited
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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 
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
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#>  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                  
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#>  ps            1.5.0   2020-12-05 [1] CRAN (R 4.0.3)
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@IndrajeetPatil
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Collaborator

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
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mtcruz commented Nov 9, 2021

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()
#> - Session info ---------------------------------------------------------------
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#>  version  R version 4.0.5 (2021-03-31)
#>  os       Windows 10 x64              
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#> 
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#> 
#> [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.

@IndrajeetPatil IndrajeetPatil reopened this Nov 9, 2021
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@kassambara @const-ae @IndrajeetPatil @HannesOberreiter @shiyun09 @mtcruz