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ggsurvplot_facet() says it supports numeric/text input to pval argument, but it doesn't. #636

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DesiQuintans opened this issue Dec 19, 2023 · 0 comments
Open

ggsurvplot_facet() says it supports numeric/text input to pval argument, but it doesn't. #636

DesiQuintans opened this issue Dec 19, 2023 · 0 comments

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@DesiQuintans
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Expected behavior

The docs for the pval argument in ggsurvplot_facet() are copy-pasted from ggsurvplot(). They say:

pval: logical value, a numeric or a string. If logical and TRUE, the p-value is added on the plot. If numeric, than the computet p-value is substituted with the one passed with this parameter. If character, then the customized string appears on the plot. See examples - Example 3.

This suggests that giving a vector of new values will insert those values in each facet.

Actual behavior/steps to reproduce

library(survival)
library(survminer)
#> Loading required package: ggplot2
#> Loading required package: ggpubr
#> 
#> Attaching package: 'survminer'
#> The following object is masked from 'package:survival':
#> 
#>     myeloma

# Facet by one grouping variables: rx
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
fit <- survfit( Surv(time, status) ~ sex, data = colon )
ggsurvplot_facet(fit, colon, facet.by = "rx",
                palette = "jco", pval = TRUE)
#> Warning: `as.tibble()` was deprecated in tibble 2.0.0.
#> ℹ Please use `as_tibble()` instead.
#> ℹ The signature and semantics have changed, see `?as_tibble`.
#> ℹ The deprecated feature was likely used in the survminer package.
#>   Please report the issue at <https://github.com/kassambara/survminer/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `select_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `select()` instead.
#> ℹ The deprecated feature was likely used in the survminer package.
#>   Please report the issue at <https://github.com/kassambara/survminer/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.

# Facet by two grouping variables: rx and adhere
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
ggsurvplot_facet(fit, colon, facet.by = c("rx", "adhere"),
                palette = "jco", pval = 0.34534)

# Another fit
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::
fit2 <- survfit( Surv(time, status) ~ sex + rx, data = colon )
ggsurvplot_facet(fit2, colon, facet.by = "adhere",
                palette = "jco", pval = "test")
#> Error in if (pval) {: argument is not interpretable as logical

Created on 2023-12-19 with reprex v2.0.2

session_info()

# please paste here the result of
─ Session info ──────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31 ucrt)
 os       Windows 11 x64 (build 22621)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_Australia.utf8
 ctype    English_Australia.utf8
 tz       Australia/Sydney
 date     2023-12-19
 rstudio  2023.09.0+463 Desert Sunflower (desktop)
 pandoc   3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ──────────────────────────────────────────────────────────
 package     * version   date (UTC) lib source
 abind         1.4-5     2016-07-21 [1] CRAN (R 4.3.0)
 backports     1.4.1     2021-12-13 [1] CRAN (R 4.3.0)
 broom         1.0.5     2023-06-09 [1] CRAN (R 4.3.1)
 cachem        1.0.8     2023-05-01 [1] CRAN (R 4.3.0)
 callr         3.7.3     2022-11-02 [1] CRAN (R 4.3.0)
 car           3.1-2     2023-03-30 [1] CRAN (R 4.3.0)
 carData       3.0-5     2022-01-06 [1] CRAN (R 4.3.0)
 cli           3.6.2     2023-12-11 [1] CRAN (R 4.3.2)
 clipr         0.8.0     2022-02-22 [1] CRAN (R 4.3.1)
 colorspace    2.1-0     2023-01-23 [1] CRAN (R 4.3.0)
 commonmark    1.9.0     2023-03-17 [1] CRAN (R 4.3.0)
 crayon        1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
 curl          5.1.0     2023-10-02 [1] CRAN (R 4.3.2)
 data.table    1.14.10   2023-12-08 [1] CRAN (R 4.3.2)
 desc          1.4.3     2023-12-10 [1] CRAN (R 4.3.2)
 devtools      2.4.5     2022-10-11 [1] CRAN (R 4.3.0)
 digest        0.6.33    2023-07-07 [1] CRAN (R 4.3.1)
 dplyr         1.1.4     2023-11-17 [1] CRAN (R 4.3.2)
 ellipsis      0.3.2     2021-04-29 [1] CRAN (R 4.3.0)
 evaluate      0.23      2023-11-01 [1] CRAN (R 4.3.2)
 fansi         1.0.6     2023-12-08 [1] CRAN (R 4.3.2)
 farver        2.1.1     2022-07-06 [1] CRAN (R 4.3.0)
 fastmap       1.1.1     2023-02-24 [1] CRAN (R 4.3.0)
 fs            1.6.3     2023-07-20 [1] CRAN (R 4.3.1)
 generics      0.1.3     2022-07-05 [1] CRAN (R 4.3.0)
 ggplot2     * 3.4.4     2023-10-12 [1] CRAN (R 4.3.1)
 ggpubr      * 0.6.0     2023-02-10 [1] CRAN (R 4.3.1)
 ggsci         3.0.0     2023-03-08 [1] CRAN (R 4.3.1)
 ggsignif      0.6.4     2022-10-13 [1] CRAN (R 4.3.1)
 ggtext        0.1.2     2022-09-16 [1] CRAN (R 4.3.2)
 glue          1.6.2     2022-02-24 [1] CRAN (R 4.3.0)
 gridExtra     2.3       2017-09-09 [1] CRAN (R 4.3.0)
 gridtext      0.1.5     2022-09-16 [1] CRAN (R 4.3.2)
 gtable        0.3.4     2023-08-21 [1] CRAN (R 4.3.1)
 htmltools     0.5.7     2023-11-03 [1] CRAN (R 4.3.2)
 htmlwidgets   1.6.3     2023-11-22 [1] CRAN (R 4.3.2)
 httpuv        1.6.12    2023-10-23 [1] CRAN (R 4.3.2)
 km.ci         0.5-6     2022-04-06 [1] CRAN (R 4.3.2)
 KMsurv        0.1-5     2012-12-03 [1] CRAN (R 4.3.1)
 knitr         1.45      2023-10-30 [1] CRAN (R 4.3.2)
 labeling      0.4.3     2023-08-29 [1] CRAN (R 4.3.1)
 later         1.3.1     2023-05-02 [1] CRAN (R 4.3.0)
 lattice       0.22-5    2023-10-24 [2] CRAN (R 4.3.2)
 lifecycle     1.0.4     2023-11-07 [1] CRAN (R 4.3.2)
 magrittr      2.0.3     2022-03-30 [1] CRAN (R 4.3.0)
 markdown      1.12      2023-12-06 [1] CRAN (R 4.3.2)
 Matrix        1.6-3     2023-11-14 [1] CRAN (R 4.3.2)
 memoise       2.0.1     2021-11-26 [1] CRAN (R 4.3.0)
 mime          0.12      2021-09-28 [1] CRAN (R 4.3.0)
 miniUI        0.1.1.1   2018-05-18 [1] CRAN (R 4.3.0)
 munsell       0.5.0     2018-06-12 [1] CRAN (R 4.3.0)
 pillar        1.9.0     2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild      1.4.3     2023-12-10 [1] CRAN (R 4.3.2)
 pkgconfig     2.0.3     2019-09-22 [1] CRAN (R 4.3.0)
 pkgload       1.3.3     2023-09-22 [1] CRAN (R 4.3.2)
 processx      3.8.3     2023-12-10 [1] CRAN (R 4.3.2)
 profvis       0.3.8     2023-05-02 [1] CRAN (R 4.3.0)
 promises      1.2.1     2023-08-10 [1] CRAN (R 4.3.2)
 ps            1.7.5     2023-04-18 [1] CRAN (R 4.3.0)
 purrr         1.0.2     2023-08-10 [1] CRAN (R 4.3.1)
 R.cache       0.16.0    2022-07-21 [1] CRAN (R 4.3.0)
 R.methodsS3   1.8.2     2022-06-13 [1] CRAN (R 4.3.0)
 R.oo          1.25.0    2022-06-12 [1] CRAN (R 4.3.0)
 R.utils       2.12.3    2023-11-18 [1] CRAN (R 4.3.2)
 R6            2.5.1     2021-08-19 [1] CRAN (R 4.3.0)
 ragg          1.2.7     2023-12-11 [1] CRAN (R 4.3.2)
 Rcpp          1.0.11    2023-07-06 [1] CRAN (R 4.3.1)
 remotes       2.4.2.1   2023-07-18 [1] CRAN (R 4.3.1)
 reprex        2.0.2     2022-08-17 [1] CRAN (R 4.3.0)
 rlang         1.1.2     2023-11-04 [1] CRAN (R 4.3.2)
 rmarkdown     2.25      2023-09-18 [1] CRAN (R 4.3.2)
 rstatix       0.7.2     2023-02-01 [1] CRAN (R 4.3.1)
 rstudioapi    0.15.0    2023-07-07 [1] CRAN (R 4.3.1)
 scales        1.3.0     2023-11-28 [1] CRAN (R 4.3.1)
 sessioninfo   1.2.2     2021-12-06 [1] CRAN (R 4.3.0)
 shiny         1.8.0     2023-11-17 [1] CRAN (R 4.3.2)
 stringi       1.8.3     2023-12-11 [1] CRAN (R 4.3.2)
 stringr       1.5.1     2023-11-14 [1] CRAN (R 4.3.2)
 styler        1.10.2    2023-08-29 [1] CRAN (R 4.3.2)
 survival    * 3.5-7     2023-08-14 [2] CRAN (R 4.3.2)
 survminer   * 0.4.9.999 2023-12-19 [1] Github (kassambara/survminer@64de674)
 survMisc      0.5.6     2022-04-07 [1] CRAN (R 4.3.2)
 systemfonts   1.0.5     2023-10-09 [1] CRAN (R 4.3.1)
 textshaping   0.3.7     2023-10-09 [1] CRAN (R 4.3.2)
 tibble        3.2.1     2023-03-20 [1] CRAN (R 4.3.0)
 tidyr         1.3.0     2023-01-24 [1] CRAN (R 4.3.0)
 tidyselect    1.2.0     2022-10-10 [1] CRAN (R 4.3.0)
 urlchecker    1.0.1     2021-11-30 [1] CRAN (R 4.3.0)
 usethis       2.2.2     2023-07-06 [1] CRAN (R 4.3.1)
 utf8          1.2.4     2023-10-22 [1] CRAN (R 4.3.2)
 vctrs         0.6.5     2023-12-01 [1] CRAN (R 4.3.2)
 withr         2.5.2     2023-10-30 [1] CRAN (R 4.3.2)
 xfun          0.41      2023-11-01 [1] CRAN (R 4.3.2)
 xml2          1.3.6     2023-12-04 [1] CRAN (R 4.3.2)
 xtable        1.8-4     2019-04-21 [1] CRAN (R 4.3.0)
 yaml          2.3.8     2023-12-11 [1] CRAN (R 4.3.2)
 zoo           1.8-12    2023-04-13 [1] CRAN (R 4.3.0)

 [1] C:/Users/dqui6184/AppData/Local/R/win-library/4.3
 [2] C:/Program Files/R/R-4.3.2/library

─────────────────────────────────────────────────────────────────────
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@DesiQuintans