DG3

Barplots of Categorical Variables

The graphs below summarize the distribution of a categorical biomarker variable as barplots, either in the overall population or by one or more categorical clinical variables.

We will use the cadsl data set from the random.cdisc.data package to illustrate the graph and will select on the biomarker evaluable population with BEP01FL. The column BMRKR2 contains the biomarker values on a categorical scale. We will use ARM as categorical clinical variable.

Code

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

adsl <- random.cdisc.data::cadsl %>%
  df_explicit_na() %>%
  filter(BEP01FL == "Y")

Here below the code for a simple barplot showing the counts of the categories.

Code

graph <- ggplot(adsl, aes(BMRKR2)) +
  geom_bar()

graph

We can customize the labels of the axes.

Code

graph +
  scale_x_discrete(
    breaks = c("LOW", "MEDIUM", "HIGH"),
    labels = c("Low", "Medium", "High"),
    name = "Biomarker"
  ) +
  scale_y_continuous(name = "count")

We can also add the absolute count above each of the columns.

Code

graph +
  geom_text(
    stat = "count",
    aes(label = after_stat(count)),
    vjust = -.5
  )

If instead of counts we want to display the percentages then the following options could be used:

Code

graph <- ggplot(
  adsl,
  aes(
    x = BMRKR2,
    y = prop.table(after_stat(count)),
    label = scales::percent(prop.table(after_stat(count)))
  )
) +
  geom_bar()

graph

We can customize the axes.

Code

graph +
  scale_y_continuous(
    labels = scales::percent_format(),
    name = "Proportion (%)"
  ) +
  scale_x_discrete(
    breaks = c("LOW", "MEDIUM", "HIGH"),
    labels = c("Low", "Medium", "High"),
    name = "Biomarker"
  )

We can add the percentages above each of the columns.

Code

graph +
  geom_text(
    stat = "count",
    vjust = -0.5
  )

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_0.9.5.9022       rtables_0.6.9.9014    magrittr_2.0.3       
[7] formatters_0.5.9.9001

loaded via a namespace (and not attached):
 [1] utf8_1.2.4                    generics_0.1.3               
 [3] tidyr_1.3.1                   EnvStats_3.0.0               
 [5] stringi_1.8.4                 lattice_0.22-6               
 [7] digest_0.6.37                 evaluate_0.24.0              
 [9] grid_4.4.1                    fastmap_1.2.0                
[11] jsonlite_1.8.8                Matrix_1.7-0                 
[13] backports_1.5.0               survival_3.7-0               
[15] purrr_1.0.2                   fansi_1.0.6                  
[17] scales_1.3.0                  codetools_0.2-20             
[19] Rdpack_2.6.1                  cli_3.6.3                    
[21] ggpp_0.5.8-1                  rlang_1.1.4                  
[23] rbibutils_2.2.16              munsell_0.5.1                
[25] splines_4.4.1                 withr_3.0.1                  
[27] yaml_2.3.10                   tools_4.4.1                  
[29] polynom_1.4-1                 checkmate_2.3.2              
[31] colorspace_2.1-1              forcats_1.0.0                
[33] ggstats_0.6.0                 broom_1.0.6                  
[35] vctrs_0.6.5                   R6_2.5.1                     
[37] lifecycle_1.0.4               stringr_1.5.1                
[39] htmlwidgets_1.6.4             MASS_7.3-61                  
[41] pkgconfig_2.0.3               pillar_1.9.0                 
[43] gtable_0.3.5                  glue_1.7.0                   
[45] xfun_0.47                     tibble_3.2.1                 
[47] tidyselect_1.2.1              knitr_1.48                   
[49] farver_2.1.2                  htmltools_0.5.8.1            
[51] labeling_0.4.3                rmarkdown_2.28               
[53] random.cdisc.data_0.3.15.9009 compiler_4.4.1

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