Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

error when adding geom_signif to a plot #46

Open
captcoma opened this issue Aug 17, 2018 · 4 comments
Open

error when adding geom_signif to a plot #46

captcoma opened this issue Aug 17, 2018 · 4 comments
Labels
bug

Comments

@captcoma
Copy link

captcoma commented Aug 17, 2018 •
edited
Loading

Dear Constantin

Thank you very much for your package ggsignif, I very appreciate it.
I try to add results from chi-square test to a ggplot and it was mentioned, that I could use ggsignif:

https://stackoverflow.com/questions/51886623/compare-dependent-proportions-in-a-ggplot

Moreover I found your adivce to use geom_signif

#23

However, If i add this to my plot:

geom_signif(data = annotation_df,
              aes(annotations = annotations, xmin = xmin, xmax = xmax, y_position = y_position),
              manual = TRUE)


df <- data.frame(timepoint=rep(0:2, each=10),response=c("A","B","A","A","A","A","A","A","B","B","A","A","A","A","A","A","A","B","B","B","A","B","B","B","B","B","A","B","B","B"),variable=rep(c("var1","var2"),each=5, 3), subject=rep(1:5,6))
df$timepoint <- factor(df$timepoint, level=c(1,0,2), labels=c("method_A","baseline","method_B"))

df %>% add_count(timepoint,variable,response) %>% add_count(timepoint,variable) %>% mutate(freq=n/nn*100) %>% mutate(total=1) -> df

stats <-data.frame(xmax=c(rep(c("baseline","method_B"),2)))
stats %>% mutate(xmin=as.factor(c(rep(c("method_A","baseline"),2)))) %>% 
  mutate(annotations=c("1","0.2","1","0.5")) %>% 
  mutate(y_position=5) %>% 
  mutate(variable=as.factor(c("var1","var1","var2","var2"))) -> annotation_df

ggplot(df,
       aes(x = timepoint, stratum = response, alluvium = subject,
           y = total, 
           fill = response, label = paste(freq,"%") )) +
  geom_flow() +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum", size = 3) +
  theme(legend.position = "none") +
  geom_signif(data = annotation_df,
              aes(annotations = annotations, xmin = xmin, xmax = xmax, y_position = y_position),
              manual = TRUE) +
  facet_wrap(~variable)

I get this error:
Warning: Ignoring unknown aesthetics: annotations, xmin, xmax, y_position
Error in FUN(X[[i]], ...) : object 'response' not found

If i leave out geom_signif(...) everything works.
Thank you for any advice,
Jacob
@muhark
Copy link

muhark commented Dec 10, 2020

Running into the same issue. Pretty sure it's related to #63, wasn't able to make that solution work for me though.

@IndrajeetPatil
Copy link
Collaborator

Can reproduce:

library(tidyverse)
library(ggsignif)
library(ggalluvial)

df <- data.frame(
  timepoint = rep(0:2, each = 10),
  response = c("A", "B", "A", "A", "A", "A", "A", "A", "B", "B", "A", "A", "A", "A", "A", "A", "A", "B", "B", "B", "A", "B", "B", "B", "B", "B", "A", "B", "B", "B"),
  variable = rep(c("var1", "var2"), each = 5, 3),
  subject = rep(1:5, 6)
)

df$timepoint <- factor(df$timepoint,
  level = c(1, 0, 2),
  labels = c("method_A", "baseline", "method_B")
)

df %>%
  add_count(timepoint, variable, response) %>%
  add_count(timepoint, variable) %>%
  mutate(freq = n / nn * 100) %>%
  mutate(total = 1) -> df
#> Storing counts in `nn`, as `n` already present in input
#> ℹ Use `name = "new_name"` to pick a new name.

stats <- data.frame(xmax = c(rep(c("baseline", "method_B"), 2)))
stats %>%
  mutate(xmin = as.factor(c(rep(c("method_A", "baseline"), 2)))) %>%
  mutate(annotations = c("1", "0.2", "1", "0.5")) %>%
  mutate(y_position = 5) %>%
  mutate(variable = as.factor(c("var1", "var1", "var2", "var2"))) -> annotation_df

# without
ggplot(
  df,
  aes(
    x = timepoint, stratum = response, alluvium = subject,
    y = total,
    fill = response, label = paste(freq, "%")
  )
) +
  geom_flow() +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum", size = 3) +
  theme(legend.position = "none") +
  facet_wrap(~variable)

# with
ggplot(
  df,
  aes(
    x = timepoint, stratum = response, alluvium = subject,
    y = total,
    fill = response, label = paste(freq, "%")
  )
) +
  geom_flow() +
  geom_stratum(alpha = .5) +
  geom_text(stat = "stratum", size = 3) +
  theme(legend.position = "none") +
  geom_signif(
    data = annotation_df,
    aes(annotations = annotations, xmin = xmin, xmax = xmax, y_position = y_position),
    manual = TRUE
  ) +
  facet_wrap(~variable)
#> Warning: Ignoring unknown aesthetics: annotations, xmin, xmax, y_position
#> Error in FUN(X[[i]], ...): object 'response' not found

Created on 2021-01-13 by the reprex package (v0.3.0)

Session info 
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)
#>  backports     1.2.1   2020-12-09 [1] CRAN (R 4.0.3)
#>  broom         0.7.3   2020-12-16 [1] CRAN (R 4.0.3)
#>  callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.2)
#>  cellranger    1.1.0   2016-07-27 [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)
#>  DBI           1.1.0   2019-12-15 [1] CRAN (R 4.0.2)
#>  dbplyr        2.0.0   2020-11-03 [1] CRAN (R 4.0.2)
#>  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)
#>  forcats     * 0.5.0   2020-03-01 [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)
#>  ggalluvial  * 0.12.3  2020-12-05 [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)
#>  haven         2.3.1   2020-06-01 [1] CRAN (R 4.0.2)
#>  highr         0.8     2019-03-20 [1] CRAN (R 4.0.2)
#>  hms           0.5.3   2020-01-08 [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)
#>  jsonlite      1.7.2   2020-12-09 [1] CRAN (R 4.0.3)
#>  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)
#>  lubridate     1.7.9.2 2020-11-13 [1] CRAN (R 4.0.3)
#>  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)
#>  modelr        0.1.8   2020-05-19 [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)
#>  Rcpp          1.0.5   2020-07-06 [1] CRAN (R 4.0.2)
#>  readr       * 1.4.0   2020-10-05 [1] CRAN (R 4.0.2)
#>  readxl        1.3.1   2019-03-13 [1] CRAN (R 4.0.2)
#>  remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.2)
#>  reprex        0.3.0   2019-05-16 [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)
#>  rvest         0.3.6   2020-07-25 [1] CRAN (R 4.0.2)
#>  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)
#>  tidyr       * 1.1.2   2020-08-27 [1] CRAN (R 4.0.2)
#>  tidyselect    1.1.0   2020-05-11 [1] CRAN (R 4.0.2)
#>  tidyverse   * 1.3.0   2019-11-21 [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

@aubreyghoward
Copy link

aubreyghoward commented Aug 6, 2021 •
edited
Loading

I would like to add the the error in (FUN(X[[i]], ...) is caused by a lack of the specification on dataframe supplying the significance values for all required terms in the facted plot. In the above example, there is not a term in the significance dataframe for "response". This can be solved by supplying the discrete arguments for the comparisons you intend to plot. Please see this example code using diamonds below, which I hope clarifies the issue:


library(ggplot2)
library(ggsignif)
rm(list = ls())

diamonds.abbv <- diamonds[diamonds$clarity == c("I1","SI2"),]

df.sig <- data.frame( start = c(0.8, 1.2), 
                        end = c(1.2,1.8),
                        y = c(3,3),
                        cut = c("Fair","Good"),
                        star = c("D", "E"),
                        label = c("#1", "#2"),
                       clarity = c("I1","I1"))
ggplot(data = diamonds.abbv, mapping = aes( x = color,
                                       y = carat,
                                       fill = clarity))+
         geom_boxplot()+
  facet_wrap(~cut)

ggplot(data = diamonds.abbv, mapping = aes( x = color,
                                            y = carat,
                                            fill = clarity))+
  geom_boxplot()+
  facet_wrap(~cut)+
  geom_signif(data = df.sig, manual = TRUE, 
              mapping = aes(xmin = star, xmax = end, y_position = y, annotations = label))
##end run

However, I still get the following error:

[Warning message:
Ignoring unknown aesthetics: xmin, xmax, y_position, annotations ]

@bersbersbers
Copy link

The original error is also explained here:
https://stackoverflow.com/a/40391432/880783

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@IndrajeetPatil @bersbersbers @captcoma @aubreyghoward @muhark