Nothing
## ----options, echo = FALSE----------------------------------------------------------------------------------------------------------------------------------------------
library(knitr)
opts_chunk$set(
echo = TRUE, results = 'markup', warning = FALSE,
# stop document execution if error (not the default)
error = FALSE,
message = FALSE, cache = FALSE,
fig.width = 8, fig.height = 7,
fig.path = "./figures_vignette/",
fig.align = 'center')
options(width = 170)
# instead of warn = 0 by default
# include warnings when they occur in the document
options(warn = 1)
## ----loadPackages-------------------------------------------------------------------------------------------------------------------------------------------------------
library(inTextSummaryTable)
library(clinUtils)
library(pander)
## ----loadData-----------------------------------------------------------------------------------------------------------------------------------------------------------
# load example data
data(dataADaMCDISCP01)
dataAll <- dataADaMCDISCP01
labelVars <- attr(dataAll, "labelVars")
## ----visualization-extractData------------------------------------------------------------------------------------------------------------------------------------------
dataLB <- subset(dataAll$ADLBC, grepl("Baseline|Week", AVISIT))
dataLB$AVISIT <- with(dataLB, reorder(trimws(AVISIT), AVISITN))
dataLB$TRTA <- with(dataLB, reorder(TRTA, TRTAN))
summaryTableDf <- computeSummaryStatisticsTable(
data = dataLB,
var = "AVAL",
rowVar = c("PARCAT1", "PARAM"),
colVar = c("TRTA", "AVISIT")
)
## ----visualization-a4document-------------------------------------------------------------------------------------------------------------------------------------------
# create the plot
dataPlot <- subset(
summaryTableDf,
!isTotal &
PARAM == "Alanine Aminotransferase (U/L)"
)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN"
)
## ----visualization-presentation-----------------------------------------------------------------------------------------------------------------------------------------
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----getVignetteAesthetics, eval = FALSE--------------------------------------------------------------------------------------------------------------------------------
#
# vignette("inTextSummaryTable-aesthetics", "inTextSummaryTable")
#
## ----getVignetteClinUtils, eval = FALSE---------------------------------------------------------------------------------------------------------------------------------
#
# vignette("clinUtils-vignette", "clinUtils")
#
## ----visualization-customColorFromArgument------------------------------------------------------------------------------------------------------------------------------
# custom color palette by setting a named vector of colors
customColorPalette <- c(
`Xanomeline Low Dose` = "green",
`Xanomeline High Dose` = "red",
`Placebo` = "blue"
)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
colorPalette = customColorPalette,
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----visualization-customShapeFromArgument------------------------------------------------------------------------------------------------------------------------------
# custom shape palette
customShapePalette <- c(15, 17, 19)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
shapePalette = customShapePalette,
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
# custom linetype palette
customLinetypePalette <- c("twodash", "dotted", "longdash")
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
linetypePalette = customLinetypePalette,
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----exampleLoadingPackageAndOptions, eval = FALSE----------------------------------------------------------------------------------------------------------------------
#
# # this is OK
# library(inTextSummaryTable)
# options(inTextSummaryTable.colors.plot = customColorPalette)
#
# # this does NOT set your custom palette
# options(inTextSummaryTable.colors.plot = customColorPalette)
# library(inTextSummaryTable)
#
## ----visualization-customColorFromOptions-------------------------------------------------------------------------------------------------------------------------------
# custom color palette by setting a simple vector of colors
customColorPalette <- c("blue", "green", "orange")
options(inTextSummaryTable.colors.plot = customColorPalette)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
# custom color palette by setting a named vector of colors
customColorPalette <- c(
`Xanomeline Low Dose` = "green",
`Xanomeline High Dose` = "red",
`Placebo` = "purple"
)
options(inTextSummaryTable.colors.plot = customColorPalette)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----visualization-customShapeFromOptions-------------------------------------------------------------------------------------------------------------------------------
# custom shape palette
customShapePalette <- c(17, 19, 22)
options(inTextSummaryTable.shapes.plot = customShapePalette)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
# custom linetype palette
customLinetypePalette <- c("dotted", "longdash", "solid")
options(inTextSummaryTable.linetypes.plot = customLinetypePalette)
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----visualization-backDefaultPalettes----------------------------------------------------------------------------------------------------------------------------------
options(inTextSummaryTable.colors.plot = clinColors)
options(inTextSummaryTable.shapes.plot = clinShapes)
options(inTextSummaryTable.linetypes.plot = clinLinetypes)
## ----visualization-table------------------------------------------------------------------------------------------------------------------------------------------------
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = NULL,
style = "presentation"
)
## ----visualization-facets, out.width = "100%", fig.height = 9, fig.width = 9--------------------------------------------------------------------------------------------
# create the plot
dataPlotFacets <- subset(
summaryTableDf,
!isTotal &
PARAM %in% c(
"Alanine Aminotransferase (U/L)",
"Albumin (g/L)",
"Bilirubin (umol/L)",
"Calcium (mmol/L)"
)
)
subjectProfileSummaryPlot(
data = dataPlotFacets,
xVar = "AVISIT",
colorVar = "TRTA",
labelVars = labelVars,
facetVar = c("PARCAT1", "PARAM"),
useLinetype = TRUE
)
## ----visualization-otherInputs------------------------------------------------------------------------------------------------------------------------------------------
# plot the median instead of mean
# no error bars
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
meanVar = "statMedian",
seVar = NULL,
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
# plot the mean with standard deviation
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
seVar = "statSD",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
# change labels
subjectProfileSummaryPlot(
data = dataPlot,
xVar = "AVISIT",
xLab = "Time points",
yLab = "Mean and Standard Errors",
title = "Title of the plot",
colorVar = "TRTA",
labelVars = labelVars,
useLinetype = TRUE,
tableText = "statN",
style = "presentation"
)
## ----includeSessionInfo, echo = FALSE-----------------------------------------------------------------------------------------------------------------------------------
pander(sessionInfo())
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.