sunburstClinData: Sunburst interactive plot.

In clinDataReview: Clinical Data Review Tool

Sunburst interactive plot.

Description

Note: the table and plot are not (yet) linked.

Usage

sunburstClinData(...)

Arguments

...

Arguments passed on to plotCountClinData colorVar (optional) String with coloring variable (NULL by default). By default, the treemap is colored based by section. colorRange (optional) Numeric vector of length 2 with range for the color variable, in case it is a numeric variable. vars Character vector with variables of data containing the groups. If multiple, they should be specified in hierarchical order (from parent to child node). varsLab Named character vector with labels for vars. valueVar String with numeric variable of data containing the value to display. valueLab String with label for the valueVar variable. valueType String with type of values in valueVar (branchvalues of the plot_ly) function), among others: 'total' (default, only if sum(child) <= to parent) or 'relative'. 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. table Logical, if TRUE (FALSE by default) returns also a datatable containing the plot data. (The plot and the table are not linked.) data Data.frame with data. 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. width Numeric, width of the plot in pixels, 800 by default. height Numeric, height of the plot in pixels, 500 by default. hoverVars Character vector with variable(s) to be displayed in the hover, by default any position (and axis) and aesthetic variables displayed in the plot. hoverLab Named character vector with labels for hoverVars. labelVars Named character vector containing variable labels. 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. title String with title for the plot. titleExtra String with extra title for the plot (appended after 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. subtitle String with subtitle. The subtitle is included at the top left of the plot, below the title. 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. watermark (optional) String with path to a file containing a watermark. tableButton Logical, if TRUE (by default) the table is included within an HTML button. tableVars Character vector with variables to be included in the table. tableLab Named character vector with labels for each tableVars. tablePars List with parameters passed to the getClinDT function.

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)

Laure Cougnaud

See Also

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

Examples

library(clinUtils)

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

dataAE <- dataADaMCDISCP01$ADAE
dataDM <- dataADaMCDISCP01$ADSL

## example of basic sunburst:

# sunburst takes as input table with counts
if (requireNamespace("inTextSummaryTable", quietly = TRUE)) {

# total counts: Safety Analysis Set (patients with start date for the first treatment)
dataTotal <- subset(dataDM, RFSTDTC != "")

# compute adverse event table
tableAE <- inTextSummaryTable::getSummaryStatisticsTable(
		
	data = dataAE,
	rowVar = c("AESOC", "AEDECOD"),
	dataTotal = dataTotal,
	rowOrder = "total",
	labelVars = labelVars,
	stats = inTextSummaryTable::getStats("count"),
	
	# plotly treemap requires records (rows) for each group
	rowVarTotalInclude = "AEDECOD",
	outputType = "data.frame-base"

)

dataSunburst <- tableAE

dataSunburst$n <- as.numeric(dataSunburst$n)

# create plot
sunburstClinData(
	data = dataSunburst,
	vars = c("AESOC", "AEDECOD"),
	valueVar = "n",
    valueLab = "Number of patients with adverse events"
)

## example where sum(counts) of child = counts of parent

# counts of patients per arm/site
tableDM <- inTextSummaryTable::getSummaryStatisticsTable(
	data = dataDM,
	rowVar = c("ARM", "SITEID"),
	labelVars = labelVars,
	# plotly treemap requires records (rows) for each group
	rowVarTotalInclude = "SITEID",
	rowTotalInclude = TRUE,
	outputType = "data.frame-base"
)
tableDM$statN <- as.numeric(tableDM$statN)

# create the plot
sunburstClinData(
	data = tableDM,
	vars = c("ARM", "SITEID"),
	valueVar = "statN", valueLab = "Counts of patients",
	valueType = "total",
	caption = "The sectors are colored by category.",
	subtitle = "Group: treatment and site"
)

}

clinDataReview documentation built on April 12, 2025, 1:14 a.m.