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Biomarker Screen Figure

Source: R/Visualize_BiomarkerScreen.R
Visualize_BiomarkerScreen.Rd

A static ggplot2 figure of the screen the biomarker screen opens on: one row per biomarker, R's estimate and its interval on one shared axis, with the estimate, the unadjusted p-value and the adjusted one printed beside each row's name. The rows run from the largest estimate down, as the screen sorts them by default. It is the screen Widget_BiomarkerScreen() draws in the browser, from the same settings, and its rows are Analyze_Screen()'s on the same frame. A hazard ratio is drawn on a logarithmic axis, with 1 marked.

Usage

Visualize_BiomarkerScreen(
  dfResults,
  dfParticipants = NULL,
  lSettings = list(),
  dfOutcomes = NULL
)

Arguments

dfResults

data.frame Long-format results, one row per participant, biomarker and visit. Column names are supplied by lSettings; the defaults expect USUBJID/TEST/STRESN/VISIT/VISITNUM/STRESU, the columns of Synthetic_Results.

dfParticipants

data.frame One row per participant, or NULL. With it the chart has filters, and the columns of groups and the numbers it offers are read from it. Default: NULL.

lSettings

list bio.viz biomarker screen settings, as Widget_BiomarkerScreen() takes them, and title, subtitle and footnotes. Default: list().

dfOutcomes

data.frame An outcomes table, one row per participant and endpoint with a time and a flag, as Widget_StratifiedSurvival() takes it, or NULL. With it the screen offers a hazard ratio. It comes after lSettings, so a call written for v0.1.0 works as it did. Default: NULL.

Value

A ggplot object.

Titles and footnotes

The settings title, subtitle and footnotes are text with named placeholders, as for Visualize_GroupComparison(). This figure fills {heading} (what the rows are), {comparison}, {visit}, {endpoint} (a hazard ratio's endpoint), {biomarkers} (how many are screened), {n} (the participants in the frame), {filters}, {date} and {version}.

See also

Widget_BiomarkerScreen(), its interactive twin.

Other figures: Run_Specifications(), Visualize_AssociationScatter(), Visualize_CorrelationMatrix(), Visualize_CrossTab(), Visualize_GroupComparison(), Visualize_StratifiedSurvival()

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  Visualize_BiomarkerScreen(
    Synthetic_Results,
    Synthetic_Participants,
    lSettings = list(visit = "Week 4", value_type = "change", group_by = "ARM", title = "{heading}")
  )
}