TLG Catalog - Stable
  • Stable
    • Dev
  1. Graphs
  2. Pharmacokinetic
  3. PKPG04
  • Introduction

  • Tables
    • ADA
      • ADAT01
      • ADAT02
      • ADAT03
      • ADAT04A
      • ADAT04B
    • Adverse Events
      • AET01
      • AET01_AESI
      • AET02
      • AET02_SMQ
      • AET03
      • AET04
      • AET04_PI
      • AET05
      • AET05_ALL
      • AET06
      • AET06_SMQ
      • AET07
      • AET09
      • AET09_SMQ
      • AET10
    • Concomitant Medications
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      • DTHT01
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      • DISCLOSUREST01
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      • EUDRAT02
    • Disposition
      • DST01
      • PDT01
      • PDT02
    • ECG
      • EGT01
      • EGT02
      • EGT03
      • EGT04
      • EGT05_QTCAT
    • Efficacy
      • AOVT01
      • AOVT02
      • AOVT03
      • CFBT01
      • CMHT01
      • COXT01
      • COXT02
      • DORT01
      • LGRT02
      • MMRMT01
      • ONCT05
      • RATET01
      • RBMIT01
      • RSPT01
      • TTET01
    • Exposure
      • EXT01
    • Lab Results
      • LBT01
      • LBT02
      • LBT03
      • LBT04
      • LBT05
      • LBT06
      • LBT07
      • LBT08
      • LBT09
      • LBT10
      • LBT10_BL
      • LBT11
      • LBT11_BL
      • LBT12
      • LBT12_BL
      • LBT13
      • LBT14
      • LBT15
    • Medical History
      • MHT01
    • Pharmacokinetic
      • PKCT01
      • PKPT02
      • PKPT03
      • PKPT04
      • PKPT05
      • PKPT06
      • PKPT07
      • PKPT08
      • PKPT11
    • Risk Management Plan
      • RMPT01
      • RMPT03
      • RMPT04
      • RMPT05
      • RMPT06
    • Safety
      • ENTXX
    • Vital Signs
      • VST01
      • VST02
  • Listings
    • ADA
      • ADAL02
    • Adverse Events
      • AEL01
      • AEL01_NOLLT
      • AEL02
      • AEL02_ED
      • AEL03
      • AEL04
    • Concomitant Medications
      • CML01
      • CML02A_GL
      • CML02B_GL
    • Development Safety Update Report
      • DSUR4
    • Disposition
      • DSL01
      • DSL02
    • ECG
      • EGL01
    • Efficacy
      • ONCL01
    • Exposure
      • EXL01
    • Lab Results
      • LBL01
      • LBL01_RLS
      • LBL02A
      • LBL02A_RLS
      • LBL02B
    • Medical History
      • MHL01
    • Pharmacokinetic
      • ADAL01
      • PKCL01
      • PKCL02
      • PKPL01
      • PKPL02
      • PKPL04
    • Vital Signs
      • VSL01
  • Graphs
    • Efficacy
      • FSTG01
      • FSTG02
      • KMG01
      • MMRMG01
      • MMRMG02
    • Other
      • BRG01
      • BWG01
      • CIG01
      • IPPG01
      • LTG01
      • MNG01
    • Pharmacokinetic
      • PKCG01
      • PKCG02
      • PKCG03
      • PKPG01
      • PKPG02
      • PKPG03
      • PKPG04
      • PKPG06

  • Appendix
    • Reproducibility

  • Index

On this page

  • Output
  • Reproducibility
    • Timestamp
    • Session Info
    • .lock file
  • Edit this page
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  1. Graphs
  2. Pharmacokinetic
  3. PKPG04

PKPG04

Box Plot of Pharmacokinetic Parameters by Visit – Plasma


Output

  • Plot of CMAX by Visit
  • Data Setup
  • Preview
  • Try this using WebR
Code
# filtered parameter
adpp <- adpp %>% filter(toupper(PARAMCD) == "CMAX" & toupper(PPSPEC) == "PLASMA")

use_title <- paste0("Boxplot of ", as.character(unique(adpp$PARAM)), " by Visit")
use_subtitle <- paste0(
  "Analyte:\nPK Parameter: ",
  as.character(unique(adpp$PARAM)),
  " (",
  as.character(unique(adpp$AVALU)),
  ")"
)
use_footnote <- "Program: \nOutput:"

p <- ggplot(adpp, aes(x = AVISIT, y = AVAL, fill = ACTARM)) +
  geom_boxplot(outlier.size = 2) +
  stat_boxplot(geom = "errorbar") +
  stat_summary(geom = "point", fun = "mean", col = "black", size = 5, shape = 8, position = position_dodge(0.75)) +
  geom_text_repel(
    data = . %>% dplyr::group_by(AVISIT, ACTARM) %>% dplyr::filter(AVAL %in% boxplot.stats(AVAL)$out),
    aes(x = AVISIT, y = AVAL, label = SUBJID, color = ACTARM),
    size = 3, hjust = -0.2, position = position_dodge(0.75)
  ) +
  labs(
    title = use_title,
    subtitle = use_subtitle,
    caption = use_footnote,
    x = "Visit",
    y = paste0(as.character(unique(adpp$PARAM)), " (", as.character(unique(adpp$AVALU)), ")")
  ) +
  theme(plot.caption = element_text(hjust = 0)) +
  theme_nest()

plot <- p + geom_point(aes(fill = ACTARM), size = 2, shape = 21, position = position_dodge(0.75))
plot

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Code
library(tern)
library(dplyr)
library(ggplot2)
library(ggrepel)
library(nestcolor)

adpp <- random.cdisc.data::cadpp

Reproducibility

Timestamp

[1] "2025-07-12 18:02:29 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-07-12
 pandoc   3.7.0.2 @ /usr/bin/ (via rmarkdown)
 quarto   1.7.32 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package           * version date (UTC) lib source
 backports           1.5.0   2024-05-23 [1] RSPM
 brio                1.1.5   2024-04-24 [1] RSPM
 broom               1.0.8   2025-03-28 [1] RSPM
 checkmate           2.3.2   2024-07-29 [1] RSPM
 cli                 3.6.5   2025-04-23 [1] RSPM
 codetools           0.2-20  2024-03-31 [2] CRAN (R 4.5.0)
 curl                6.4.0   2025-06-22 [1] RSPM
 dichromat           2.0-0.1 2022-05-02 [1] CRAN (R 4.5.0)
 digest              0.6.37  2024-08-19 [1] RSPM
 dplyr             * 1.1.4   2023-11-17 [1] RSPM
 evaluate            1.0.4   2025-06-18 [1] RSPM
 farver              2.1.2   2024-05-13 [1] RSPM
 fastmap             1.2.0   2024-05-15 [1] RSPM
 formatters        * 0.5.11  2025-04-09 [1] RSPM
 generics            0.1.4   2025-05-09 [1] RSPM
 ggplot2           * 3.5.2   2025-04-09 [1] RSPM
 ggrepel           * 0.9.6   2024-09-07 [1] RSPM
 glue                1.8.0   2024-09-30 [1] RSPM
 gtable              0.3.6   2024-10-25 [1] RSPM
 htmltools           0.5.8.1 2024-04-04 [1] RSPM
 htmlwidgets         1.6.4   2023-12-06 [1] RSPM
 jsonlite            2.0.0   2025-03-27 [1] RSPM
 knitr               1.50    2025-03-16 [1] RSPM
 labeling            0.4.3   2023-08-29 [1] RSPM
 lattice             0.22-7  2025-04-02 [2] CRAN (R 4.5.0)
 lifecycle           1.0.4   2023-11-07 [1] RSPM
 magrittr          * 2.0.3   2022-03-30 [1] RSPM
 Matrix              1.7-3   2025-03-11 [1] CRAN (R 4.5.0)
 nestcolor         * 0.1.3   2025-01-21 [1] RSPM
 pillar              1.11.0  2025-07-04 [1] RSPM
 pkgcache            2.2.4   2025-05-26 [1] RSPM
 pkgconfig           2.0.3   2019-09-22 [1] RSPM
 processx            3.8.6   2025-02-21 [1] RSPM
 ps                  1.9.1   2025-04-12 [1] RSPM
 purrr               1.1.0   2025-07-10 [1] RSPM
 R6                  2.6.1   2025-02-15 [1] RSPM
 random.cdisc.data   0.3.16  2024-10-10 [1] RSPM
 rbibutils           2.3     2024-10-04 [1] RSPM
 RColorBrewer        1.1-3   2022-04-03 [1] RSPM
 Rcpp                1.1.0   2025-07-02 [1] RSPM
 Rdpack              2.6.4   2025-04-09 [1] RSPM
 rlang               1.1.6   2025-04-11 [1] RSPM
 rmarkdown           2.29    2024-11-04 [1] RSPM
 rtables           * 0.6.13  2025-06-19 [1] RSPM
 scales              1.4.0   2025-04-24 [1] RSPM
 sessioninfo         1.2.3   2025-02-05 [1] any (@1.2.3)
 stringi             1.8.7   2025-03-27 [1] RSPM
 stringr             1.5.1   2023-11-14 [1] RSPM
 survival            3.8-3   2024-12-17 [2] CRAN (R 4.5.0)
 tern              * 0.9.9   2025-06-20 [1] RSPM
 testthat            3.2.3   2025-01-13 [1] RSPM
 tibble              3.3.0   2025-06-08 [1] RSPM
 tidyr               1.3.1   2024-01-24 [1] RSPM
 tidyselect          1.2.1   2024-03-11 [1] RSPM
 vctrs               0.6.5   2023-12-01 [1] RSPM
 withr               3.0.2   2024-10-28 [1] RSPM
 xfun                0.52    2025-04-02 [1] RSPM
 yaml                2.3.10  2024-07-26 [1] RSPM

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library
 [3] /github/home/R/x86_64-pc-linux-gnu-library/4.5
 * ── Packages attached to the search path.

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

.lock file

Download the .lock file and use renv::restore() on it to recreate environment used to generate this website.

Download

PKPG03
PKPG06
Source Code
---
title: PKPG04
subtitle: Box Plot of Pharmacokinetic Parameters by Visit -- Plasma
---

------------------------------------------------------------------------

{{< include ../../_utils/envir_hook.qmd >}}

```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(tern)
library(dplyr)
library(ggplot2)
library(ggrepel)
library(nestcolor)

adpp <- random.cdisc.data::cadpp
```

```{r include = FALSE}
webr_code_labels <- c("setup")
```

{{< include ../../_utils/webr_no_include.qmd >}}

## Output

:::: panel-tabset
## Plot of CMAX by Visit

::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview

```{r plot1, test = list(plot_v1 = "plot")}
# filtered parameter
adpp <- adpp %>% filter(toupper(PARAMCD) == "CMAX" & toupper(PPSPEC) == "PLASMA")

use_title <- paste0("Boxplot of ", as.character(unique(adpp$PARAM)), " by Visit")
use_subtitle <- paste0(
  "Analyte:\nPK Parameter: ",
  as.character(unique(adpp$PARAM)),
  " (",
  as.character(unique(adpp$AVALU)),
  ")"
)
use_footnote <- "Program: \nOutput:"

p <- ggplot(adpp, aes(x = AVISIT, y = AVAL, fill = ACTARM)) +
  geom_boxplot(outlier.size = 2) +
  stat_boxplot(geom = "errorbar") +
  stat_summary(geom = "point", fun = "mean", col = "black", size = 5, shape = 8, position = position_dodge(0.75)) +
  geom_text_repel(
    data = . %>% dplyr::group_by(AVISIT, ACTARM) %>% dplyr::filter(AVAL %in% boxplot.stats(AVAL)$out),
    aes(x = AVISIT, y = AVAL, label = SUBJID, color = ACTARM),
    size = 3, hjust = -0.2, position = position_dodge(0.75)
  ) +
  labs(
    title = use_title,
    subtitle = use_subtitle,
    caption = use_footnote,
    x = "Visit",
    y = paste0(as.character(unique(adpp$PARAM)), " (", as.character(unique(adpp$AVALU)), ")")
  ) +
  theme(plot.caption = element_text(hjust = 0)) +
  theme_nest()

plot <- p + geom_point(aes(fill = ACTARM), size = 2, shape = 21, position = position_dodge(0.75))
plot
```

```{r include = FALSE}
webr_code_labels <- c("plot1")
```

{{< include ../../_utils/webr.qmd >}}
:::

## Data Setup

```{r setup}
#| code-fold: show
```
::::

{{< include ../../_utils/save_results.qmd >}}

{{< include ../../repro.qmd >}}

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