RG3

Response Graphs Comparing BEP vs. Overall Population

The same setup as in RG1 is used.

For ggplot() used in all analyses, we add by = BMEASIFL in the aesthetics to support the calculation of proportions using geom_text(stat = "prop").

Code

library(tern)
library(ggplot2.utils)
library(dplyr)

adrs <- random.cdisc.data::cadrs %>%
  df_explicit_na() %>%
  mutate(
    AVALC = ordered(AVALC, levels = c("<Missing>", "NE", "PD", "SD", "PR", "CR")),
    AVALC_BIN = fct_collapse_only(
      AVALC,
      Yes = c("CR", "PR"),
      No = c("PD", "SD", "NE", "<Missing>")
    ),
    ARM_BIN = fct_collapse_only(
      ARM,
      Ctrl = c("B: Placebo"),
      Trt = c("A: Drug X", "C: Combination")
    )
  ) %>%
  filter(PARAMCD == "BESRSPI", BMEASIFL == "Y")

In this example we can use the facet_grid() layer with the margins = TRUE option to compare the responses between the biomarker evaluable population (BEP) and the overall population.

Code

graph <- ggplot(adrs, aes(BMEASIFL, fill = AVALC_BIN, by = BMEASIFL)) +
  geom_bar(position = "fill") +
  geom_text(stat = "prop", position = position_fill(.5), colour = "white") +
  scale_y_continuous(
    labels = scales::percent,
    name = "Proportion %"
  ) +
  scale_x_discrete(labels = NULL) +
  xlab(NULL)

graph +
  facet_grid(BEP01FL ~ ., margins = TRUE)

In this example we compare the responses across treatment arms between the biomarker evaluable population and the full population. We can add the option margins = TRUE option within the facet_grid() layer to obtain the responses across all treatment arms and their combination within each of the populations.

Code

graph +
  facet_grid(BEP01FL ~ ARM_BIN, margins = TRUE)

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         ggplot2.utils_0.3.2 ggplot2_3.5.1      
[4] tern_0.9.5          rtables_0.6.9       magrittr_2.0.3     
[7] formatters_0.5.9   

loaded via a namespace (and not attached):
 [1] utf8_1.2.4               generics_0.1.3           tidyr_1.3.1             
 [4] EnvStats_3.0.0           stringi_1.8.4            lattice_0.22-6          
 [7] digest_0.6.37            evaluate_0.24.0          grid_4.4.1              
[10] fastmap_1.2.0            jsonlite_1.8.8           Matrix_1.7-0            
[13] backports_1.5.0          survival_3.7-0           purrr_1.0.2             
[16] fansi_1.0.6              viridisLite_0.4.2        scales_1.3.0            
[19] codetools_0.2-20         Rdpack_2.6.1             cli_3.6.3               
[22] ggpp_0.5.8-1             rlang_1.1.4              rbibutils_2.2.16        
[25] munsell_0.5.1            splines_4.4.1            withr_3.0.1             
[28] yaml_2.3.10              tools_4.4.1              polynom_1.4-1           
[31] checkmate_2.3.2          colorspace_2.1-1         forcats_1.0.0           
[34] ggstats_0.6.0            broom_1.0.6              vctrs_0.6.5             
[37] R6_2.5.1                 lifecycle_1.0.4          stringr_1.5.1           
[40] htmlwidgets_1.6.4        MASS_7.3-61              pkgconfig_2.0.3         
[43] pillar_1.9.0             gtable_0.3.5             glue_1.7.0              
[46] xfun_0.47                tibble_3.2.1             tidyselect_1.2.1        
[49] knitr_1.48               farver_2.1.2             htmltools_0.5.8.1       
[52] labeling_0.4.3           rmarkdown_2.28           random.cdisc.data_0.3.15
[55] compiler_4.4.1

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