Available options

The inTextSummaryTable package has the following options:

• inTextSummaryTable.colors.table.presentation

• inTextSummaryTable.pageDim.presentation

• inTextSummaryTable.colors.plot

• inTextSummaryTable.shapes.plot

• inTextSummaryTable.linetypes.plot

The options with the wording colors.table.presentation and pageDim.presentation define the color scheme for tables and the dimensions of the page in a presentation, respectively.

Instead, the options with colors.plot, shapes.plot and linetype.plot set up the palettes for the visualization functionalities.

Note that the options have to be defined after loading the package. This because when loading the package, the default global options for palettes will overwrite the custom palettes.

In this way, you can see how the options are visible after loading the package:

library(inTextSummaryTable)

# options for color scheme in in presentations
options("inTextSummaryTable.colors.table.presentation")

## $inTextSummaryTable.colors.table.presentation
##                    header          headerBackground headerBackgroundHighlight                      body           bodyBackground1           bodyBackground2 
##                 "#FFFFFF"               "#32648EFF"               "#287D8EFF"                 "#000000"                 "#D9D9D9"                 "#D9D9D9" 
##  bodyBackgroundHighlight1  bodyBackgroundHighlight2                    footer          footerBackground                      line 
##               "#DCE318FF"               "#DCE318FF"                 "#000000"                 "#FFFFFF"                 "#FFFFFF"

# options for colors in plots: viridis palette
options("inTextSummaryTable.colors.plot")

## $inTextSummaryTable.colors.plot
## function (n, alpha = 1, begin = 0, end = 1, direction = 1, option = "D") 
## {
##     if (begin < 0 | begin > 1 | end < 0 | end > 1) {
##         stop("begin and end must be in [0,1]")
##     }
##     if (abs(direction) != 1) {
##         stop("direction must be 1 or -1")
##     }
##     if (n == 0) {
##         return(character(0))
##     }
##     if (direction == -1) {
##         tmp <- begin
##         begin <- end
##         end <- tmp
##     }
##     option <- switch(EXPR = option, A = "A", magma = "A", B = "B", 
##         inferno = "B", C = "C", plasma = "C", D = "D", viridis = "D", 
##         E = "E", cividis = "E", F = "F", rocket = "F", G = "G", 
##         mako = "G", H = "H", turbo = "H", {
##             warning(paste0("Option '", option, "' does not exist. Defaulting to 'viridis'."))
##             "D"
##         })
##     map <- viridisLite::viridis.map[viridisLite::viridis.map$opt == 
##         option, ]
##     map_cols <- grDevices::rgb(map$R, map$G, map$B)
##     fn_cols <- grDevices::colorRamp(map_cols, space = "Lab", 
##         interpolate = "spline")
##     cols <- fn_cols(seq(begin, end, length.out = n))/255
##     grDevices::rgb(cols[, 1], cols[, 2], cols[, 3], alpha = alpha)
## }
## <bytecode: 0x558c24486988>
## <environment: namespace:viridisLite>

# options for shapes in plots
options("inTextSummaryTable.shapes.plot")

## $inTextSummaryTable.shapes.plot
##  [1] 21 22 23 24 25  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 17 18 19

# options for linetypes in plots
options("inTextSummaryTable.linetypes.plot")

## $inTextSummaryTable.linetypes.plot
## [1] "solid"    "dashed"   "dotdash"  "twodash"  "dotted"   "longdash"

Options for reporting

In this section we discuss the options for reporting, namely the inTextSummaryTable.colors.table.presentation and inTextSummaryTable.pageDim.presentation.

# default report style
getSummaryStatisticsTable(
    data = data.frame(USUBJID = c(1, 2)),
    style = "report" 
)

# default presentation style
getSummaryStatisticsTable(
    data = data.frame(USUBJID = c(1, 2)),
    style = "presentation" 
)

# create named vector
customColorTable <- c(
    # black text in the header
    'header' = "#000000",
    # green background in the header
    'headerBackground' = "#74D055FF",
    # black text in the body
    'body' = "#000000", 
    # yellow background for all rows
    'bodyBackground1' = "#FDE725FF",
    'bodyBackground2' = "#FDE725FF",
    # black footer
    'footer' = "#000000",
    # white footer background
    'footerBackground' = "#FFFFFF",
    # black line for footer
    'line' = "#000000"
)
# set options
options(inTextSummaryTable.colors.table.presentation = customColorTable)
# create the table
getSummaryStatisticsTable(
    data = data.frame(USUBJID = c(1, 2)),
    style = "presentation" 
)

# default page dimension of a powerpoint created with Rmd
getOption("inTextSummaryTable.pageDim.presentation")

## [1]  7.5 10.0

# set custom dimension of page for presentation
# in this example, the dimension is the widescreen size
pageDimCustom <- c(7.5, 13.32)
options(inTextSummaryTable.pageDim.presentation = pageDimCustom)
getOption("inTextSummaryTable.pageDim.presentation")

## [1]  7.50 13.32

Options for visualization

The defaults palettes for visualization are retrieved from the clinUtils package.

If you wish to know more about those palettes, we refer to the vignette of clinUtils available with

vignette("clinUtils-vignette", "clinUtils")

Below a demonstration with a dummy data set.

# default colors, shapes and linetypes
summaryTable <- data.frame(
    visit = c(1, 2, 1, 2), 
    TRT = c("A", "A", "B", "B"),
    statMean = rnorm(4)
)    
subjectProfileSummaryPlot(
    data = summaryTable,
    xVar = "visit", 
    colorVar = "TRT" 
)

For the visualization, the same spirit of the tables applies. The user can specify a vector of colors, shapes or linetypes. The vector do not necessarly have to be named.

# specify colors
options(inTextSummaryTable.colors.plot = c("red", "green"))
subjectProfileSummaryPlot(
    data = summaryTable,
    xVar = "visit", 
    colorVar = "TRT" 
)

# specify shape
options(inTextSummaryTable.shapes.plot = c("circle", "square"))
subjectProfileSummaryPlot(
    data = summaryTable,
    xVar = "visit", 
    colorVar = "TRT" 
)

# specify linetypes
options(inTextSummaryTable.linetypes.plot = c("dotdash", "longdash"))
subjectProfileSummaryPlot(
    data = summaryTable,
    xVar = "visit", 
    colorVar = "TRT" 
)

Set back default palettes

There is always to possibility to switch back to the default palettes of the package:

options(inTextSummaryTable.colors.table.presentation = tableColorsPresentation)
options(inTextSummaryTable.colors.plot = clinUtils::clinColors)
options(inTextSummaryTable.shapes.plot = clinUtils::clinShapes)
options(inTextSummaryTable.linetypes.plot = clinUtils::clinLinetypes)

Set up specific palettes

Page dimensions in report/presentation

The function getDimPage extracts dimensions available for a content in a report or presentation, e.g. to specify the maximal width of a figure in A4 report or for a presentation.

# a4 format with one 1 inch margin
getDimPage(type = "width", style = "report")

## [1] 6.267717

getDimPage(type = "height", style = "report")

## [1] 9.692913

# Presentation format (according to template) with one 1 inch margin
getDimPage(type = "width", style = "presentation")

## [1] 11.32

getDimPage(type = "height", style = "presentation")

## [1] 5.5

Appendix