---
title: "Introduction to 'parallelPlot'"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to 'parallelPlot'}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7
)
```

```{r setup}
library(parallelPlot)
```

## Basic usage (dataset uses `factor` type)

```{r}
parallelPlot(iris)
```

'species' column is of factor type and has box representation for its categories.

## `refColumnDim` argument (referenced column is categorical)

```{r}
parallelPlot(iris, refColumnDim = "Species")
```

Each trace has a color depending of its 'species' value.

## `categoricalCS` argument

```{r}
parallelPlot(iris, refColumnDim = "Species", categoricalCS = "Set1")
```

Colors used for categories are not the same as previously
(supported values: `Category10`, `Accent`, `Dark2`, `Paired`, `Set1`).

## `refColumnDim` argument (referenced column is continuous)

```{r}
parallelPlot(iris, refColumnDim = "Sepal.Length")
```

Each trace has a color depending of its 'Sepal.Length' value.

## `continuousCS` argument

```{r}
parallelPlot(iris, refColumnDim = "Sepal.Length", continuousCS = "YlOrRd")
```

Colors used for lines are not the same as previously. Supported values: `Viridis`, `Inferno`, `Magma`, `Plasma`, `Warm`, `Cool`, `Rainbow`, `CubehelixDefault`, `Blues`, `Greens`, `Greys`, `Oranges`, `Purples`, `Reds`, `BuGn`, `BuPu`, `GnBu`, `OrRd`, `PuBuGn`, `PuBu`, `PuRd`, `RdBu`, `RdPu`, `YlGnBu`, `YlGn`, `YlOrBr`, `YlOrRd`

## Basic usage (dataset doesn't use `factor` type)

```{r}
parallelPlot(mtcars)
```

Several columns are of numerical type but should be of factor type (for example `cyl`).

## `categorical` argument

```{r}
categorical <- list(cyl = c(4, 6, 8), vs = c(0, 1), am = c(0, 1), gear = 3:5, carb = 1:8)
parallelPlot(mtcars, categorical = categorical, refColumnDim = "cyl")
```

`cyl` and four last columns have a box representation for categories.

## `categoriesRep` argument

```{r}
categorical <- list(cyl = c(4, 6, 8), vs = c(0, 1), am = c(0, 1), gear = 3:5, carb = 1:8)
parallelPlot(
  mtcars,
  categorical = categorical,
  refColumnDim = "cyl",
  categoriesRep = "EquallySizedBoxes"
)
```

Within a category column, the height assigned to each category can either be equal for each category (`EquallySizedBoxes`) or calculated to reflect the proportion of lines passing through each category (`EquallySpacedLines`).

## `arrangeMethod` argument

```{r}
categorical <- list(cyl = c(4, 6, 8), vs = c(0, 1), am = c(0, 1), gear = 3:5, carb = 1:8)
parallelPlot(
  mtcars,
  categorical = categorical,
  refColumnDim = "cyl",
  arrangeMethod = "fromLeft"
)
```

Within a category box, the position of lines is computed to minimize crossings on the left of the box. `arrangeMethod` can also be set to `fromRight` to minimize crossings on the left of the box (default behavior). `fromBoth` allows to merge the two behaviors (see next example). To turn this ordering off (for example for performance reasons), `arrangeMethod` can also be set to `fromNone`.

## `arrangeMethod` argument (using `fromBoth`)

```{r}
categorical <- list(cyl = c(4, 6, 8), vs = c(0, 1), am = c(0, 1), gear = 3:5, carb = 1:8)
parallelPlot(
  mtcars,
  categorical = categorical,
  refColumnDim = "cyl",
  arrangeMethod = "fromBoth"
)
```

Within a category box, lines have an incoming point and an outgoing point; these points are ordered to minimize crossings on the left and on the right of the box.

## `inputColumns` argument

```{r}
categorical <- list(cyl = c(4, 6, 8), vs = c(0, 1), am = c(0, 1), gear = 3:5, carb = 1:8)
inputColumns <- c("mpg", "disp", "drat", "qsec", "am", "gear", "carb")
parallelPlot(
  mtcars,
  categorical = categorical,
  inputColumns = inputColumns,
  refColumnDim = "cyl"
)
```

The column name is blue for outputs and green for inputs (in shiny mode, inputs can be edited).

## `histoVisibility` argument

```{r}
histoVisibility <- rep(TRUE, ncol(iris))
parallelPlot(iris, histoVisibility = histoVisibility)
```

An histogram is displayed for each column.

## `invertedAxes` argument

```{r}
invertedAxes <- c("Sepal.Width")
parallelPlot(iris, invertedAxes = invertedAxes)
```

Axis of second column is inverted (a sign '↓' is added at the beginning of the column header).

## `cutoffs` argument

```{r}
histoVisibility <- names(iris) # same as `rep(TRUE, ncol(iris))`
cutoffs <- list(Sepal.Length = list(c(6, 7)), Species = c("virginica", "setosa"))
parallelPlot(iris, histoVisibility = histoVisibility, cutoffs = cutoffs)
```

Lines which are not kept by cutoffs are shaded; an histogram for each column is displayed considering only kept lines.

## `refRowIndex` argument

```{r}
parallelPlot(iris, refRowIndex = 1)
```

Axes are shifted vertically in such a way that first trace of the dataset looks horizontal.

## `rotateTitle` argument

```{r}
parallelPlot(iris, refColumnDim = "Species", rotateTitle = TRUE)
```

Column names are rotated (can be useful for long column names).

## `columnLabels` argument

```{r}
columnLabels <- gsub("\\.", "<br>", colnames(iris))
parallelPlot(iris, refColumnDim = "Species", columnLabels = columnLabels)
```

Given names are displayed in place of column names found in dataset; `<br>` is used to insert line breaks.

## `cssRules` argument

```{r}
parallelPlot(iris, cssRules = list(
  "svg" = "background: #C2C2C2", # Set background of plot to grey
  ".axisLabel" = c("fill: red", "font-size: 1.8em"), # Set title of axes red and greater
  ".tick text" = "font-size: 1.8em", # Set text of axes ticks greater
  ".plotGroup path" = "opacity: 0.25", # Make lines less opaque
  ".xValue" = "color: orange", # Set color for x values in tooltip
  ".xName" = "display: table" # Trick to have x values on a new line
))
```

Apply CSS to the plot. CSS is a simple way to describe how elements on a web page should be displayed (position, color, size, etc.). 
See the page [Styling 'parallelPlot'](styling-parallelPlot.html) for more details.

## `sliderPosition` argument

```{r}
parallelPlot(iris, sliderPosition = list(
  dimCount = 3, # Number of columns to show
  startingDimIndex = 2 # Index of first shown column
))
```

Visible columns starts at second column and three columns are represented.

## `controlWidgets` argument

```{r}
parallelPlot(iris, refColumnDim = "Species", controlWidgets = TRUE, height = 350)
```

Widgets are added above the graph, allowing to modify some of its attributes.
