Hepatic Safety Explorer

eDISH scatter of peak liver measures with Hy’s Law quadrants and participant drill-down to standardized values by study day.

The chart below is live — rendered by the safety.viz hepExplorer module on the package’s example data, with the full control sidebar. measure_values maps the ALT/AST/TB/ALP keys onto this dataset’s measure names, and the visit sequence stands in for study day.

Render this report from a workflow

The same chart ships as a gsm-idiom report workflow. Run it with gsm.core::RunWorkflow() to produce a standalone HTML report, or use the matching runner script:

lWorkflow <- yaml::read_yaml(
  system.file("workflow", "3_reports", "hep_explorer.yaml", package = "gsm.safety")
)

gsm.core::RunWorkflow(
  lWorkflow = lWorkflow,
  lData = list(dfResults = ExampleData("adbds"))
)

Rscript inst/examples/hep-explorer.R <output-dir>

The full hep_explorer.yaml workflow

meta:
  Type: Report
  ID: hep_explorer
  Output: html
  Name: Hepatic Safety Explorer Report
  Description: Interactive safety.viz eDISH hepatic safety explorer with Hy's Law quadrants and participant drill-down.
  lSettings:
    studyday_col: VISITNUM
    visit_col: VISIT
    visitn_col: VISITNUM
    measure_values:
      ALT: Alanine Aminotransferase
      AST: Aspartate Aminotransferase
      TB: Bilirubin
      ALP: Alkaline Phosphatase
    filters:
      - value_col: SEX
        label: Sex
      - value_col: ARM
        label: Treatment Group
    groups:
      - value_col: ARM
        label: Treatment Group
      - value_col: SEX
        label: Sex
spec:
  dfResults:
    USUBJID:
      type: character
    TEST:
      type: character
    STRESN:
      type: numeric
    STNRHI:
      type: numeric
steps:
  - output: strOutputDir
    name: getwd
  - output: lWidget
    name: gsm.safety::Widget_HepExplorer
    params:
      dfResults: dfResults
      lSettings: lSettings
  - output: strReportPath
    name: gsm.safety::SaveWidgetReport
    params:
      widget: lWidget
      strOutputDir: strOutputDir
      strOutputFile: ID

The live chart

library(gsm.safety)

dfResults <- ExampleData("adbds")

Widget_HepExplorer(
  dfResults,
  lSettings = list(
    studyday_col = "VISITNUM",
    visit_col = "VISIT",
    visitn_col = "VISITNUM",
    measure_values = list(
      ALT = "Alanine Aminotransferase",
      AST = "Aspartate Aminotransferase",
      TB = "Bilirubin",
      ALP = "Alkaline Phosphatase"
    ),
    filters = list(
      list(value_col = "SEX", label = "Sex"),
      list(value_col = "ARM", label = "Treatment Group")
    ),
    groups = list(
      list(value_col = "ARM", label = "Treatment Group"),
      list(value_col = "SEX", label = "Sex")
    )
  )
)