KG4A

Change Color and Line Type in Kaplan-Meier Graph by Treatment Arm and Biomarker Subgroups

A setup similar to KG1 is used, with some additional data manipulation steps to first binarize the continuous biomarker and the treatment arm variables, and then combine both into a new interaction variable ARM_BMRKR2. Since we are using biomarker information, we filter on the biomarker evaluable population using the flag variable BEP01FL.

Code

library(tern)
library(dplyr)

adtte <- random.cdisc.data::cadtte %>%
  df_explicit_na() %>%
  filter(PARAMCD == "OS" & BEP01FL == "Y") %>%
  mutate(
    is_event = CNSR == 0,
    BMRKR2_BIN = fct_collapse_only(
      BMRKR2,
      High = c("HIGH"),
      Low = c("MEDIUM", "LOW")
    ),
    ARM_BIN = fct_collapse_only(
      ARM,
      CTRL = c("B: Placebo"),
      TRT = c("A: Drug X", "C: Combination")
    ),
    ARM_BMRKR2 = interaction(ARM_BIN, BMRKR2_BIN)
  )

variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM_BMRKR2")

We can customize the color and line type used in the graph with the col and lty arguments of g_km(). We can first check the level order of the ARM_BMRKR2 factor variable to know which color and line type order we need.

Code

levels(adtte$ARM_BMRKR2)

[1] "CTRL.High" "TRT.High"  "CTRL.Low"  "TRT.Low"

Code

g_km(
  df = adtte,
  variables = variables,
  annot_surv_med = TRUE,
  col = c("green", "orange", "green", "orange"),
  lty = c(5, 5, 3, 3)
)

Code

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] dplyr_1.1.4           tern_0.9.5.9022       rtables_0.6.9.9014   
[4] magrittr_2.0.3        formatters_0.5.9.9001

loaded via a namespace (and not attached):
 [1] Matrix_1.7-0                  gtable_0.3.5                 
 [3] jsonlite_1.8.8                compiler_4.4.1               
 [5] tidyselect_1.2.1              stringr_1.5.1                
 [7] tidyr_1.3.1                   splines_4.4.1                
 [9] scales_1.3.0                  yaml_2.3.10                  
[11] fastmap_1.2.0                 lattice_0.22-6               
[13] ggplot2_3.5.1                 R6_2.5.1                     
[15] labeling_0.4.3                generics_0.1.3               
[17] knitr_1.48                    forcats_1.0.0                
[19] rbibutils_2.2.16              htmlwidgets_1.6.4            
[21] backports_1.5.0               checkmate_2.3.2              
[23] tibble_3.2.1                  munsell_0.5.1                
[25] pillar_1.9.0                  rlang_1.1.4                  
[27] utf8_1.2.4                    broom_1.0.6                  
[29] stringi_1.8.4                 xfun_0.47                    
[31] cli_3.6.3                     withr_3.0.1                  
[33] Rdpack_2.6.1                  digest_0.6.37                
[35] grid_4.4.1                    cowplot_1.1.3                
[37] lifecycle_1.0.4               vctrs_0.6.5                  
[39] evaluate_0.24.0               glue_1.7.0                   
[41] farver_2.1.2                  codetools_0.2-20             
[43] survival_3.7-0                random.cdisc.data_0.3.15.9009
[45] fansi_1.0.6                   colorspace_2.1-1             
[47] purrr_1.0.2                   rmarkdown_2.28               
[49] tools_4.4.1                   pkgconfig_2.0.3              
[51] htmltools_0.5.8.1

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