barplotClinData: Barplot visualization of clinical data.

Description

Barplot visualization of clinical data.

Usage

barplotClinData(
  data,
  xVar,
  yVar,
  xLab = getLabelVar(xVar, labelVars = labelVars),
  xLabVar = NULL,
  yLab = getLabelVar(yVar, labelVars = labelVars),
  yLabVar = NULL,
  colorVar = NULL,
  colorLab = getLabelVar(colorVar, labelVars = labelVars),
  colorPalette = NULL,
  barmode = "group",
  title = paste(c(paste(yLab, "vs", xLab), titleExtra), collapse = "
"),
  titleExtra = NULL,
  caption = NULL,
  subtitle = NULL,
  labelVars = NULL,
  width = NULL,
  height = NULL,
  hoverVars,
  hoverLab,
  textVar = NULL,
  pathVar = NULL,
  pathLab = getLabelVar(pathVar, labelVars = labelVars),
  table = FALSE,
  tableVars,
  tableLab,
  tableButton = TRUE,
  tablePars = list(),
  id = paste0("plotClinData", sample.int(n = 1000, size = 1)),
  selectVars = NULL,
  selectLab = getLabelVar(selectVars, labelVars = labelVars),
  watermark = NULL,
  verbose = FALSE
)

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

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.

xLabVar

(optional) Character vector with column(s) of data containing variable(s) to display in the label of the x-axis.

yLab

String with label for xVar.

yLabVar

(optional) Character vector with column(s) of data containing variable(s) to display in the label of the y-axis.

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.

barmode

String with type of barplot, either: 'group' or 'stack' (see parameter in layout).

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.

labelVars

Named character vector containing variable labels.

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.

textVar

(optional) String with a text variable, that will be displayed outside of each bar.

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.)

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.

selectVars

(optional) Character vector with variable(s) from data for which a selection box should be included. This enables to select the data displayed in the plot (and associated table).

selectLab

(Named) character vector with label for selectVars.

watermark

(optional) String with path to a file containing a watermark.

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.

Author

Laure Cougnaud

Examples

Run this code

library(clinUtils)

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

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

## example of basic barplot:

# treemap 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::computeSummaryStatisticsTable(
	data = dataAE,
	rowVar = c("AEBODSYS", "AEDECOD"),
	rowOrder = "total",
	dataTotal = dataTotal,
	labelVars = labelVars,
	stats = inTextSummaryTable::getStats("count")
)

dataPlot <- subset(tableAE, AEDECOD != "Total")

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

# create plot
barplotClinData(
	data = dataPlot,
	xVar = "AEDECOD", 
	yVar = "n", yLab = "Number of patients with adverse events",
	labelVars = labelVars
)

# add number on top of the bars
barplotClinData(
	data = dataPlot,
	xVar = "AEDECOD", 
	yVar = "n", yLab = "Number of patients with adverse events",
	textVar = "n",
	labelVars = labelVars
)

# add a selection box
if(interactive()){
  barplotClinData(
    data = dataPlot,
    xVar = "AEDECOD", 
    yVar = "n", yLab = "Number of patients with adverse events",
    labelVars = labelVars,
    selectVars = "AEBODSYS"
  )
}

# display percentage of events per severity
tableAEBySeverity <- inTextSummaryTable::computeSummaryStatisticsTable(
	data = dataAE,
	rowVar = c("AEDECOD", "AESEV"),
	dataTotal = dataTotal,
	labelVars = labelVars,
	statsPerc = "statm",
	stats = inTextSummaryTable::getStats("%m"),
	dataTotalPerc = dataAE,
	rowVarTotalPerc = "AEDECOD"
)
barplotClinData(
	data = tableAEBySeverity,
	xVar = "AEDECOD", xLab = "Adverse event term",
	yVar = "statPercm", yLab = "Percentage of adverse events",
	labelVars = labelVars,
	colorVar = "AESEV", barmode = "stack",
	hoverVar = c("AEDECOD", "AESEV", "statN", "statm", "statPercm"),
	hoverLab = c(
		labelVars["AEDECOD"],
		labelVars["AESEV"],
		statN = "Number of patients",
		statm = "Number of events",
		statPercm = "Percentage of events"
	),
	textVar = "%m",
	# add subtitle
	subtitle = "Group: severity"
)

}