---
title: "Visualization functionalities"
author: "Laure Cougnaud"
date: "`r format(Sys.Date(), '%B %d, %Y')`"
output: 
  rmarkdown::html_document:
    toc: true
    toc_float: true
    toc_depth: 5
    number_sections: true
vignette: >
  %\VignetteIndexEntry{Visualization functionalities}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

<style>
.zoomDiv {
  opacity: 0;
  position:fixed;
  top: 50%;
  left: 50%;
  z-index: 50;
  transform: translate(-50%, -50%);
  box-shadow: 0px 0px 50px #888888;
  max-height:100%; 
  overflow: scroll;
}

.zoomImg {
  width: 100%;
}
</style>


<script type="text/javascript">
  $(document).ready(function() {
    $('body').prepend("<div class=\"zoomDiv\"><img src=\"\" class=\"zoomImg\"></div>");
    // onClick function for all plots (img's)
    $('img:not(.zoomImg)').click(function() {
      $('.zoomImg').attr('src', $(this).attr('src'));
      $('.zoomDiv').css({opacity: '1', width: '60%'});
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```{r 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)

```

This vignette focuses on the visualization functionalities available within the
`inTextSummaryTable` package.

If you need to see figures bigger, just click on a graphic, and it will pop up
more readable.

Summary statistics can be visualized by:

1. **extracting the summary statistics table** with the
  `computeSummaryStatisticsTable` function (used for `getSummaryStatistics`
  function)
2. **visualizing the summary statistics via the `subjectProfileSummaryPlot`**
  function
  
By default the **`subjectProfileSummaryPlot`** plots the mean values with
**error bars** based on standard errors.

Moreover, the `subjectProfileSummaryPlot` allows the possibility to add a table
of counts of the number of subject for a specific combination of variables.

This vignette will guide the user to

* default **visualizations for A4 and presentation documents**
* **customize palettes of colors, shape, linetypes**
* **visualization with and without table of counts and by facets**
* general customizable input

However, in order to get a full overview of the functionalities the
documentation is available in the console with `? subjectProfileSummaryPlot`.

We will first create example data sets to show how the exporting functionalities
work. The data sets used here are available in the `clinUtils` package.


# Load packages and data

```{r loadPackages}

library(inTextSummaryTable)
library(clinUtils)
library(pander)

```

```{r loadData}	

# load example data
data(dataADaMCDISCP01)

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

```
  
# Compute summary statistics  
  
Below we compute summary statistics for the laboratory data set.
  
```{r 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 for A4 document

The code below shows the default visualization, which plots the **mean with
standard errors** **suitable for an A4 document**, e.g. Word/pdf.

Note that the table below the plot is based on the counts for treatment and
visit variables, as specificed in the `colVar` argument of the code chuck above
for `computeSummaryStatisticsTable`.

```{r 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 for presentation

The code below shows the default visualization **suitable for a
presentation**, either in Powerpoint or ioslides.

```{r visualization-presentation}

subjectProfileSummaryPlot(
    data = dataPlot,
    xVar = "AVISIT",
    colorVar = "TRTA",
    labelVars = labelVars,
    useLinetype = TRUE,
    tableText = "statN",
    style = "presentation"
)

```

Please note that the default font for presentation is _Tahoma_. 

If you don't have this default font available, 
the R package [_extrafont_](https://cran.r-project.org/package=extrafont)
might be useful to register fonts with your R graphics device.

# Palettes

The `inTextSummaryTable` uses default palettes available in the
`clinUtils` package.

However, palettes are fully customizable. Currently, there are two alternative
approaches to change the defaults:

* set the custom palettes as arguments in the `subjectProfileSummaryPlot`
  via the dedicated parameters **`colorPalette`**, **`shapePalette`**,
  **`linetypePalette`**
* set the **global options** into the R session.

Passing input arguments to the function might be convenient when creating one
plot.

Instead, **passing the global options is very handy when creating multiple
graphics**, so that the palettes have to be set only once at the beginning of
the R script, without the need to copy-paste input arguments in the
different visualizations.

If you want to **know more about aesthetics options of the
`inTextSummaryTable`**, there is a dedicated vignette available
[here](../doc/inTextSummaryTable-aesthetics.html)) or with

```{r getVignetteAesthetics, eval = FALSE}

vignette("inTextSummaryTable-aesthetics", "inTextSummaryTable")

```

If you want to **know more about default options from the
`clinUtils`**, you may check out the vignette of the package:

```{r getVignetteClinUtils, eval = FALSE}

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

```

Sections below show below both alternative approaches for setting the palettes. 

## Custom palettes via arguments in the function

In this section we guide on how to set custom palettes via the
`subjectProfileSummaryPlot` function.

### Color palette

This section focuses on the possibility to set the `colorPalette` argument.

```{r 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"
)

```

### Shape and linetype palettes

This section focuses on the possibility to set the `shapePalette` and
`linetypePalette` arguments.

```{r 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"
)

```

## Custom palettes via setting global options

The `inTextSummaryTable` package allows the user to define global options in
the R session.

As mentioned above, setting the global options is convenient because the
palettes have to be set only once in the R script or Rmd document.

Please note that the global options have to be set **after** loading the
package. This because when loading the package, the default global options
for palettes will overwrite the custom palettes.

Here in practice:

```{r 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)

```

### Coloring palettes

Color palettes can be set up with the `inTextSummaryTable.colors.plot` option.

```{r 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"
)

```

### Shape and linetype palettes

What shown for the color palette is consistent for shape and linetypes
palettes. In this case, the global options are called
`inTextSummaryTable.shapes.plot` and `inTextSummaryTable.linetypes.plot`.

```{r 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"
)

```

## Set back default palettes

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

```{r visualization-backDefaultPalettes}

options(inTextSummaryTable.colors.plot = clinColors)
options(inTextSummaryTable.shapes.plot = clinShapes)
options(inTextSummaryTable.linetypes.plot = clinLinetypes)

```

# Visualization without count table

The user can decide to remove the table of counts by setting the parameter
**`tableText`** to `NULL`, as the code below shows.

```{r visualization-table}

subjectProfileSummaryPlot(
    data = dataPlot,
    xVar = "AVISIT",
    colorVar = "TRTA",
    labelVars = labelVars,
    useLinetype = TRUE,
    tableText = NULL,
    style = "presentation"
)

```


# Visualization by facets

It is possible to directly plot multiple parameters with the **`facetVar`**
argument.

Please note that setting the `facetVar` is not compatible with adding a table
of counts underneath the plot.

```{r 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
)

```

# Customize your visualization

The `subjectProfileSummaryPlot` has many options! A non-exaustive demonstration
is presented below.

```{r 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"
)

```

# Appendix

## Session information

```{r includeSessionInfo, echo = FALSE}

pander(sessionInfo())

```
