boxplotClinData: Boxplot interactive plot.

In clinDataReview: Clinical Data Review Tool

Boxplot interactive plot.

Description

Boxplot interactive plot.

Usage

boxplotClinData(
  data,
  xVar,
  yVar,
  xLab = getLabelVar(xVar, labelVars = labelVars),
  yLab = getLabelVar(yVar, labelVars = labelVars),
  colorVar = NULL,
  colorLab = getLabelVar(colorVar, labelVars = labelVars),
  colorPalette = NULL,
  facetVar = NULL,
  facetLab = getLabelVar(facetVar, labelVars = labelVars),
  ncol = 1L,
  titleExtra = NULL,
  title = paste(paste(yLab, "vs", xLab, titleExtra), collapse = "<br>"),
  subtitle = NULL,
  caption = NULL,
  labelVars = NULL,
  width = NULL,
  height = NULL,
  hoverVars,
  hoverLab,
  pathVar = NULL,
  pathLab = getLabelVar(pathVar, labelVars = labelVars),
  idVar = "USUBJID",
  idLab = getLabelVar(idVar, labelVars = labelVars),
  table = FALSE,
  tableVars,
  tableLab,
  tableButton = TRUE,
  tablePars = list(),
  id = paste0("plotClinData", sample.int(n = 1000, size = 1)),
  verbose = FALSE
)

Arguments

data	Data.frame with data.
xVar	String with column of data containing x-variable.
yVar	String with column of data containing y-variable.
xLab	String with label for xVar.
yLab	String with label for xVar.
colorVar	(optional) String with color variable.
colorLab	String with label for colorVar.
colorPalette	(optional) Named character vector with color palette. If not specified, the viridis color palette is used. See clinColors.
facetVar	(optional) String with facet variable.
facetLab	String with label for facetVar.
ncol	single-length integer denoting the number of columns for the facetting.
titleExtra	String with extra title for the plot (appended after title).
title	String with title for the plot.
subtitle	String with subtitle. The subtitle is included at the top left of the plot, below the title.
caption	String with caption. The caption is included at the bottom right of the plot. Please note that this might overlap with vertical or rotated x-axis labels.
labelVars	Named character vector containing variable labels.
width	Numeric, width of the plot in pixels, 700 by default.
height	Numeric, height of the plot in pixels, 700 by default.
hoverVars	Character vector with variable(s) to be displayed in the hover, by default any position and aesthetic variables displayed in the plot.
hoverLab	Named character vector with labels for hoverVars.
pathVar	String with variable of data containing hyperlinks with path to the subject-specific report, formatted as: <a href="./path-to-report">label</a> . If multiple, they should be separated by: ', '. The report(s) will be: compressed to a zip file and downloaded if the user clicks on the 'p' (a.k.a 'profile') key when hovering on a point of the plot included in a collapsible row, and clickable with hyperlinks in the table
pathLab	String with label for pathVar, included in the collapsible row in the table.
idVar	String with variable containing subject ID.
idLab	String with label for idVar.
table	Logical, if TRUE (FALSE by default) returns also a datatable containing the plot data. (The plot and the table are not linked.)
tableVars	Character vector with variables to be included in the table.
tableLab	Named character vector with labels for each tableVars.
tableButton	Logical, if TRUE (by default) the table is included within an HTML button.
tablePars	List with parameters passed to the getClinDT function.
id	String with general id for the plot: 'id' is used as group for the SharedData 'button:[id]' is used as button ID if table is TRUE If not specified, a random id, as 'plotClinData[X]' is used.
verbose	Logical, if TRUE (FALSE by default) progress messages are printed in the current console. For the visualizations, progress messages during download of subject-specific report are displayed in the browser console.

Value

Either:

• if a table is requested: a clinDataReview object, a.k.a a list with the 'plot' (plotly object) and 'table' (datatable object)

• otherwise: a plotly object

Author(s)

Lennart Tuijnder

See Also

Other visualizations of summary statistics for clinical data: barplotClinData(), errorbarClinData(), plotCountClinData(), sunburstClinData(), treemapClinData()

Examples

library(clinUtils)

data(dataADaMCDISCP01)
labelVars <- attr(dataADaMCDISCP01, "labelVars")

## example of basic boxplot:

data <- subset(dataADaMCDISCP01$ADVS, 
	PARAMCD == "DIABP" & ANL01FL == "Y" &
	AVISIT %in% c("Baseline", "Week 2", "Week 4", "Week 6", "Week 8")
)

## example of basic boxplot:

# With color var and facet:
boxplotClinData(
	data = data,
	xVar = "AVISIT", 
	yVar = "AVAL",
	colorVar = "TRTA",
	facetVar = "ATPT",
	title = "Diastolic Blood Pressure distribution by actual visit and analysis timepoint",
	yLab = "Actual value of the Diastolic Blood Pressure parameter (mmHg)",
	labelVars = labelVars
)

# Control number of facet columns:
boxplotClinData(
	data = data,
	xVar = "AVISIT", 
	yVar = "AVAL",
	colorVar = "TRTA",
	facetVar = "ATPT",
	ncol = 2,
	title = "Diastolic Blood Pressure distribution by actual visit and analysis timepoint",
	yLab = "Actual value of the Diastolic Blood Pressure parameter (mmHg)",
	labelVars = labelVars
)

## Not run: 

# Facet or color is optional:
boxplotClinData(
	data = data,
	xVar = "AVISIT", 
	yVar = "AVAL",
	colorVar = "TRTA"
)

boxplotClinData(
	data = data,
	xVar = "AVISIT", 
	yVar = "AVAL",
	facetVar = "ATPT"
)

# add caption & subtitle
boxplotClinData(
	data = data,
	xVar = "AVISIT", 
	yVar = "AVAL",
	facetVar = "ATPT", ncol = 2,
	colorVar = "TRTA",
	title = "Diastolic Blood Pressure distribution",
	subtitle = "By actual visit and analysis timepoint",
	yLab = "Actual value of the Diastolic Blood Pressure parameter (mmHg)",
	caption = "Summary statistics are computed internally.",
	labelVars = labelVars
)


## End(Not run)

clinDataReview documentation built on March 7, 2023, 5:13 p.m.