PKCG03

Plot of Mean PK Concentration Over Time by Cohort

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Code

use_title <- "Plot of Mean (+/- SD) Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients"
use_subtitle <- "Analyte:"
use_footnote <- "Program: \nOutput:"

result <- g_lineplot(
  df = adpc,
  variables = control_lineplot_vars(
    x = "NFRLT",
    y = "AVAL",
    group_var = "ARM",
    paramcd = "PARAM",
    y_unit = "AVALU",
    subject_var = "USUBJID"
  ),
  alt_counts_df = adsl_f,
  y_lab = "Concentration",
  y_lab_add_paramcd = FALSE,
  y_lab_add_unit = TRUE,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = use_title,
  subtitle = use_subtitle,
  caption = use_footnote,
  ggtheme = theme_nest()
)

plot <- result + theme(plot.caption = element_text(hjust = 0))
plot

Experimental use!

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Preview
Try this using WebR

Code

use_title <- "Plot of Mean (+/- SD) Log-Scale Plasma Concentrations Over Time by Treatment, \nPK Evaluable Patients"
use_subtitle <- "Analyte:"
use_footnote <- "Program: \nOutput:"

adpc <- adpc %>%
  mutate(avalog = ifelse(AVAL != 0, AVAL, 0.001))

result <- g_lineplot(
  df = adpc,
  variables = control_lineplot_vars(
    x = "NFRLT",
    y = "avalog",
    group_var = "ARM",
    paramcd = "PARAM",
    y_unit = "AVALU",
    subject_var = "USUBJID"
  ),
  alt_counts_df = adsl_f,
  y_lab = "Concentration",
  y_lab_add_paramcd = FALSE,
  y_lab_add_unit = TRUE,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = use_title,
  subtitle = use_subtitle,
  caption = use_footnote,
  ggtheme = theme_nest()
)

plot <- result + theme(plot.caption = element_text(hjust = 0)) +
  ggplot2::scale_y_log10(breaks = c(0.001, 0.01, 0.1, 1, 10), labels = c(0.001, 0.01, 0.1, 1, 10))

Scale for y is already present.
Adding another scale for y, which will replace the existing scale.

Code

plot

Experimental use!

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Code

library(tern)
library(dplyr)
library(ggplot2)
library(nestcolor)

adsl_f <- random.cdisc.data::cadsl %>%
  filter(SAFFL == "Y" & ARM != "B: Placebo") %>%
  df_explicit_na()

adpc <- random.cdisc.data::cadpc %>%
  mutate(Patient_ID = sub(".*id-", "", USUBJID)) %>%
  filter(PARAM == "Plasma Drug X") %>%
  droplevels() %>%
  df_explicit_na()

Reproducibility

Timestamp

[1] "2024-11-02 17:41:17 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-11-02
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version     date (UTC) lib source
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 brio                1.1.5       2024-04-24 [1] CRAN (R 4.4.1)
 broom               1.0.7       2024-09-26 [1] CRAN (R 4.4.1)
 checkmate           2.3.2       2024-07-29 [1] CRAN (R 4.4.1)
 cli                 3.6.3       2024-06-21 [1] CRAN (R 4.4.1)
 codetools           0.2-20      2024-03-31 [2] CRAN (R 4.4.1)
 colorspace          2.1-1       2024-07-26 [1] CRAN (R 4.4.1)
 digest              0.6.37      2024-08-19 [1] CRAN (R 4.4.1)
 dplyr             * 1.1.4       2023-11-17 [1] CRAN (R 4.4.1)
 evaluate            1.0.1       2024-10-10 [1] CRAN (R 4.4.1)
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 formatters        * 0.5.9.9003  2024-11-02 [1] git2r (https://github.com/insightsengineering/formatters.git@84e8c3e)
 generics            0.1.3       2022-07-05 [1] CRAN (R 4.4.1)
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 labeling            0.4.3       2023-08-29 [1] CRAN (R 4.4.1)
 lattice             0.22-6      2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle           1.0.4       2023-11-07 [1] CRAN (R 4.4.1)
 magrittr          * 2.0.3       2022-03-30 [1] CRAN (R 4.4.1)
 Matrix              1.7-0       2024-04-26 [1] CRAN (R 4.4.1)
 munsell             0.5.1       2024-04-01 [1] CRAN (R 4.4.1)
 nestcolor         * 0.1.2.9017  2024-11-02 [1] git2r (https://github.com/insightsengineering/nestcolor.git@3d2ce62)
 pillar              1.9.0       2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig           2.0.3       2019-09-22 [1] CRAN (R 4.4.1)
 purrr               1.0.2       2023-08-10 [1] CRAN (R 4.4.1)
 R6                  2.5.1       2021-08-19 [1] CRAN (R 4.4.1)
 random.cdisc.data   0.3.16.9001 2024-11-02 [1] git2r (https://github.com/insightsengineering/random.cdisc.data.git@a65bfbe)
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 Rdpack              2.6.1       2024-08-06 [1] CRAN (R 4.4.1)
 rlang               1.1.4       2024-06-04 [1] CRAN (R 4.4.1)
 rmarkdown           2.28        2024-08-17 [1] CRAN (R 4.4.1)
 rtables           * 0.6.10.9002 2024-11-02 [1] git2r (https://github.com/insightsengineering/rtables.git@d2cc7a0)
 scales              1.3.0       2023-11-28 [1] CRAN (R 4.4.1)
 sessioninfo         1.2.2       2021-12-06 [1] CRAN (R 4.4.1)
 stringi             1.8.4       2024-05-06 [1] CRAN (R 4.4.1)
 stringr             1.5.1       2023-11-14 [1] CRAN (R 4.4.1)
 survival            3.7-0       2024-06-05 [2] CRAN (R 4.4.1)
 tern              * 0.9.6.9013  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.git@435fd51)
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 tidyr               1.3.1       2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect          1.2.1       2024-03-11 [1] CRAN (R 4.4.1)
 utf8                1.2.4       2023-10-22 [1] CRAN (R 4.4.1)
 vctrs               0.6.5       2023-12-01 [1] CRAN (R 4.4.1)
 withr               3.0.1       2024-07-31 [1] CRAN (R 4.4.1)
 xfun                0.48        2024-10-03 [1] CRAN (R 4.4.1)
 yaml                2.3.10      2024-07-26 [1] CRAN (R 4.4.1)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

──────────────────────────────────────────────────────────────────────────────

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Reproducibility

Timestamp

Session Info

.lock file

`.lock` file