R: Create an interactive table to display clinical data

getClinDT {clinUtils}

R Documentation

Create an interactive table to display clinical data

Description

This function converts a data.frame from R into a datatable object with sensitive defaults.
Extra functionalities are available to:

have columns or cells of interest that are collapsible/expandable (see expandVar/expandIdx)
group rows based on a variable (see rowGroupVar)
display a variable as barplot (with specified range of threshold) (see barVar)
hide variable(s) (see nonVisibleVar)

Usage

getClinDT(
  data,
  nonVisibleVar = NULL,
  nonVisible = NULL,
  percVar = NULL,
  barVar = NULL,
  barColorThr = NULL,
  barRange = NULL,
  filter = "top",
  searchBox = FALSE,
  pageLength,
  fixedColumns = NULL,
  columnsWidth = NULL,
  options = list(),
  expandVar = NULL,
  expandIdx = NULL,
  escape = TRUE,
  rowGroup = NULL,
  rowGroupVar = NULL,
  vAlign = "top",
  callback = NULL,
  buttons = getClinDTButtons(),
  scrollX = TRUE,
  file = NULL,
  verbose = TRUE,
  ...
)

Arguments

`data`	Data.frame, matrix or `SharedData` object with input data for the table.
`nonVisibleVar`	Character vector with column(s) in `data` to hide in the output table (column is hidden). The column(s) also get the extra attribute: `className = 'noVis'`, to ensure they are not displayed in the button to show/hide column(s).
`nonVisible`	This parameter is deprecated, use the new interface with the `nonVisibleVar` parameter. Numeric vector with column(s) in `data` to not display in the output table (column is hidden), in Javascript unit: first column is 0, second column is 1, ...
`percVar`	Character vector with percentage columns. These columns should contain the percentage from 0 to 1. The content of these colunms will be rounded to 2 digits.
`barVar`	Character vector with numeric variable of `data` which should be represented as bar in the table.
`barColorThr`	Numeric vector with threshold to consider to color the bar, either: a numeric vector of length 1, same threshold for all bars named vector with threshold for each bar, named with the variable in `barVar`
`barRange`	(optional) range for the bars, either: a numeric vector of length 2, same range for all bars list with range for each bar, named with the variable in `barVar` If not specified, the range of each `barVar` variable in `data` is used.
`filter`	String with position of the filter boxes (`filter` parameter of the `datatable` function), 'top' by default. Set to 'none' to not included any filtering boxes.
`searchBox`	Logical, if TRUE (FALSE by default) a general search box is included.
`pageLength`	Numeric with number of records to include in one page, by default set to 10. Set to Inf to include all records.
`fixedColumns`	List with fixed columns, see corresponding parameter in the `options` parameter of the `datatable` function.
`columnsWidth`	Character vector with column width, of length 1 (used for all columns) or of length: `ncol(data)`
`options`	List with additional `datatable` options. This parameter overwrites the default options set internally in the function (an indicative message mentions it if that is the case).
`expandVar`	Character vector with expandable variables of `data`. These columns won't be included in the table, but displayed for each row when the '+' icon in the first column of the table will be clicked on.
`expandIdx`	Matrix named with: 'row'/'column' containing row/column indices to expand.
`escape`	Column(s) to escape in the table (e.g. containing raw HTML code), either character, numeric or logical of length 1. See corresponding parameter in the `datatable` function.
`rowGroup`	This parameter is deprecated, please use `rowGroup` instead.
`rowGroupVar`	Character vector with colname(s) of `data` containing variables to group rows by. This creates row header containing this column. Please note that the original row order in `data` is respected, so you might want to order rows based on the grouping variables upfront.
`vAlign`	String with vertical alignment for the cells, 'top' by default.
`callback`	String with custom Javascript callback function.
`buttons`	DataTable buttons (passed to the 'buttons' element of the `options` parameter of `datatable`). See `getClinDTButtons` for the default options. To remove all buttons, set this parameter to NULL.
`scrollX`	Logical, if TRUE (by default) a horizontal scrolling bar is included. Note: this differs from the `datatable` default (FALSE), because required for `bookdown::gitbook` output if table is too wide.
`file`	(optional) String with name of html file to which the created DT should be exported.
`verbose`	Logical, if TRUE (by default) informative messages are displayed, e.g. if specified `options` overwrite the internal default.
`...`	Additional parameters for the `datatable` function, e.g table width.

Value

A datatable object.

Author(s)

Laure Cougnaud

Examples

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

# example of simple adverse event table
dataAE <- dataADaMCDISCP01$ADAE
subjectsSafety <- subset(dataADaMCDISCP01$ADSL, SAFFL == "Y")$USUBJID

# compute counts of subjects presenting each AE
tableAE <- stats::aggregate(
	USUBJID ~ AESOC:AEDECOD,
	data = dataAE, 
	FUN = function(usubjid)	length(unique(usubjid))
)
colnames(tableAE)[colnames(tableAE) == "USUBJID"] <- "N"
# and percentages
tableAE$perc <- round(tableAE$N/length(subjectsSafety)*100, 3)
# sort records in decreasing percentage
tableAE <- tableAE[order(tableAE$perc, decreasing = TRUE), ]

# extract new variables labels
tableAELabels <- getLabelVar(
	var = colnames(tableAE),
	labelVars = labelVars,
	label = c(N = '# subjects', perc = "% subjects")
)
# 'colnames' for DT should be specified as c('new name' = 'old name', ...)
tableAELabelsDT <- setNames(names(tableAELabels), tableAELabels)

## create table with bar

# default:
getClinDT(
	data = tableAE,
	barVar = "perc",
	colnames = tableAELabelsDT
)

# specify range for the bar
getClinDT(
	data = tableAE,
	filter = "none",
	barVar = "perc",
	barRange = c(0, 100),
	colnames = tableAELabelsDT
)

# change color according to threshold
getClinDT(
	data = tableAE,
	filter = "none",
	barVar = "perc",
	barColorThr = seq(from = 0, to = 100, by = 25),
	colnames = tableAELabelsDT
)

## group per system organ class (and decreasing N):
tableAESOC <- aggregate(N ~ AESOC, data = tableAE, FUN = sum)
tableAE$AESOC <- factor(tableAE$AESOC,
	levels = tableAESOC[order(tableAESOC$N, decreasing = FALSE), "AESOC"]
)
tableAE <- tableAE[order(tableAE$AESOC, tableAE$perc, decreasing = TRUE), ]
	
getClinDT(
	data = tableAE,
	filter = "none",
	barVar = "perc",
	barRange = c(0, 100),
	colnames = tableAELabelsDT,
	rowGroupVar = "AESOC",
	pageLength = Inf
)

# expand the subject ID column, will
# be accessible when clicking on the '+' button
# Format URL correctly with: 'escape',
# please note that indexing starts at 0!
getClinDT(
	data = tableAE,
	barVar = "perc",
	colnames = tableAELabelsDT,
	expandVar = "USUBJID", 
	escape = grep("USUBJID", colnames(tableAE))-1
)

# fix size for columns
getClinDT(
	data = tableAE,
	colnames = tableAELabelsDT,
	fixedColumns = list(leftColumns = 1),
	columnsWidth = c(0.1, 0.7, 0.1, 0.1),
	width = "350px" # change dimension table
)

## Not run: # due to time constraint in CRAN

# change default buttons
getClinDT(
	data = tableAE,
	colnames = tableAELabelsDT,
	# remove general filter
	filter = "none",
	# custom set of buttons
	buttons = getClinDTButtons(type = c("csv", "excel", "pdf"))
)
# add button to select columns
getClinDT(
	data = tableAE,
	colnames = tableAELabelsDT,
	# custom set of buttons
	buttons = getClinDTButtons(typeExtra = "colvis")
)
# export pdf in landscape format
buttons <- getClinDTButtons(
	opts = list(pdf = list(orientation = "landscape"))
)
getClinDT(
	data = tableAE,
	colnames = tableAELabelsDT,
	# custom set of buttons
	buttons = buttons
)

# hide the first column:
getClinDT(
	data = tableAE,
	nonVisibleVar = "AESOC"
)

# with specific caption
library(htmltools)
caption <- tags$caption(
	"Number of subjects with adverse events grouped by system organ class.",
	br(), 
	paste(
		"Percentages are based on the total number of patients having",
		"received a first study treatment."
	)
)
getClinDT(
	data = tableAE,
	filter = "none",
	barVar = "perc",
	barRange = c(0, 100),
	pageLength = Inf,
	colnames = tableAELabelsDT,
	rowGroupVar = "AESOC",
	caption = caption
)


## End(Not run)

[Package clinUtils version 0.2.0 Index]