When data is in tibble format, ggsurvplot_facet will give an error with pval = TRUE

[kaipingyang]

When data is in tibble format, ggsurvplot_facet's pval = TRUE gives the following error:
Error in xtfrm.data.frame(x) : cannot xtfrm data frames

Here's a reproducible example

library(survival)
library(survminer)
library(tidyverse)
test <- colon %>% as_tibble()
fit <- survfit( Surv(time, status) ~ sex, data = test)
ggsurvplot_facet(fit, test, facet.by = "rx",
                 palette = "jco", pval = TRUE)

#> Error in xtfrm.data.frame(x) : cannot xtfrm data frames

I looked at the source code and found that ggsurvplot_facet calls surv_group_by when pval = TRUE, and in surv_group_by there is the following:

  if(length(grouping.vars) == 1){
    grp.levels <- .levels(data[, grouping.vars])
    current.order <- grouped.d[, grouping.vars] %>% as.data.frame() %>% .[,1]
    grouped.d <- grouped.d[match(grp.levels, current.order), , drop = FALSE]
  }

Notice that data[, grouping.vars] gives inconsistent results for dataframe and tibble:
The former is a vector;
The latter is tibble.
Here's a reproducible example:

> colon[,"rx"] %>% class()
[1] "factor"
> test[,"rx"] %>% class()
[1] "tbl_df"     "tbl"        "data.frame"

survminer:::.levels() can only operate on vectors, which is the cause of the error.

survminer:::.levels(test[,"rx"])
#> Error in xtfrm.data.frame(x) : cannot xtfrm data frames

So I suggest changing grp.levels <- .levels(data[, grouping.vars]) to grp.levels <- .levels(data[[grouping.vars]]) when length(grouping.vars) == 1 in surv_group_by .

session_info()

> sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.3    forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4        purrr_1.0.2       
 [6] readr_2.1.5        tidyr_1.3.1        tibble_3.2.1       tidyverse_2.0.0    survival_3.6-4    
[11] survminer_0.5.0    ggpubr_0.6.0       ggplot2_3.5.1      gtable_0.3.5       gridExtra_2.3     
[16] forestploter_1.1.3

loaded via a namespace (and not attached):
 [1] xfun_0.45          bslib_0.7.0        teal.widgets_0.4.2 rstatix_0.7.2      lattice_0.22-6    
 [6] tzdb_0.4.0         vctrs_0.6.5        tools_4.4.1        generics_0.1.3     fansi_1.0.6       
[11] pkgconfig_2.0.3    Matrix_1.7-0       data.table_1.15.4  lifecycle_1.0.4    compiler_4.4.1    
[16] farver_2.1.2       munsell_0.5.1      ggsci_3.2.0        carData_3.0-5      httpuv_1.6.15     
[21] shinyWidgets_0.8.6 htmltools_0.5.8.1  sass_0.4.9         later_1.3.2        pillar_1.9.0      
[26] car_3.1-2          jquerylib_0.1.4    cachem_1.1.0       abind_1.4-5        mime_0.12         
[31] km.ci_0.5-6        tidyselect_1.2.1   digest_0.6.36      stringi_1.8.4      labeling_0.4.3    
[36] splines_4.4.1      fastmap_1.2.0      colorspace_2.1-0   cli_3.6.3          magrittr_2.0.3    
[41] cards_0.3.0        utf8_1.2.4         broom_1.0.6        withr_3.0.0        scales_1.3.0      
[46] promises_1.3.0     backports_1.5.0    timechange_0.3.0   ggsignif_0.6.4     hms_1.1.3         
[51] zoo_1.8-12         memoise_2.0.1      shiny_1.9.1        knitr_1.47         KMsurv_0.1-5      
[56] survMisc_0.5.6     rlang_1.1.4        Rcpp_1.0.12        xtable_1.8-4       glue_1.8.0        
[61] rstudioapi_0.16.0  jsonlite_1.8.8     R6_2.5.1