# Introduction to the transitionPlot (deprecated)

#### Max Gordon

#### 2020-07-03

# Introduction

The transitionPlot function aims at illustrating the transition between classes. The original intent was to show how self-administered the Charnley classification behaves before and after surgery. The plot is a fancier version than what can be achieved using packages such as diagram but at the cost of flexibility. The current function only allows to show a transition from one state to the next.

Note: The new Transition class will superseed the transitionPlot. See `vignette("Introduction to the Transition-class")` for more info.

# Generate some data

We will start by simulating some data similar to my article. Each observation has a sex and a Charnley class (A, B, or C). The transition is then dependent on both the sex and the Charnley class.

    set.seed(1)
    library(magrittr)
    n <- 100
    data <-
      data.frame(
        Sex = sample(c("Male", "Female"),
                     size = n,
                     replace = TRUE),
        Charnley_class = sample(c("A", "B", "C"),
                                size = n,
                                replace = TRUE))
    prob <- data.frame(
      A = 1/3 +
        (data$Sex == "Male") * .25 +
        (data$Sex != "Male") * -.25 +
        (data$Charnley_class %in% "B") * -.5 +
        (data$Charnley_class %in% "C") * -2 ,
      B = 1/3 +
        (data$Sex == "Male") * .1 +
        (data$Sex != "Male") * -.05 +
        (data$Charnley_class == "C") * -.5,
      C = 1/3 +
        (data$Sex == "Male") * -.25 +
        (data$Sex != "Male") * .25)

    # Remove negative probabilities
    prob <- t(apply(prob, 1, function(x) {
      if (any(x < 0)){
        x <- x - min(x) + .05
        }
      x
      }))

    data$Charnley_class_after <-
      apply(prob, 1, function(p)
        sample(c("A", "B", "C"),
               size = 1,
               prob = p)) %>%
      factor(levels = c("A", "B", "C"))

    # Create the transition matrix that
    # is the basis for the transition plot
    trn_mtrx <-
      with(data,
           table(Charnley_class,
                 Charnley_class_after))

    rm(prob)

# Basic use

The most simple use is to just supply the output from the `table()` call:

    library(Gmisc)
    transitionPlot(trn_mtrx)

The out of the box arrows are rather in my opinion not well suited and I have therefore developed a few alternatives:

    transitionPlot(trn_mtrx,
                   type_of_arrow = "simple")

And a fancy variant that I call gradient arrows as they have a colored gradient inside that fades into the arrow color:

    transitionPlot(trn_mtrx,
                   type_of_arrow = "gradient")

# Labels and stuff

Adding title, box labels, and customizing box text can easily be done using the `main`, `box_label`, and `box_txt`. If you provide the `box_txt` a vector it assumes the same text for both left and right boxes but you can also have separate texts as in the example below:

    output_perc <-
      function(txt, n) sprintf("%s\n[%.0f%%]", txt, n)
    box_txt <-
      cbind(mapply(output_perc,
                   txt = c("A", "B", "C"),
                   n = prop.table(rowSums(trn_mtrx))*100),
            mapply(output_perc,
                   txt = c("A", "B", "C"),
                   n = prop.table(colSums(trn_mtrx))*100))
    transitionPlot(trn_mtrx,
                   main = "Charnley class changess",
                   box_label = c("Before", "After"),
                   box_txt = box_txt,
                   cex = 1.2,
                   type_of_arrow = "simple")

# Using 3D matrices

We can enhance the data-ink ratio by adding a color split for the boxes. This works only for factors with 2 levels such as sex in our example.

    trn_mtrx_3D <-
      with(data,
           table(Charnley_class,
                 Charnley_class_after,
                 Sex))

    transitionPlot(trn_mtrx_3D,
                   fill_start_box = c("#5C246E", "#00688B"),
                   type_of_arrow = "simple")

The gradient arrow is most useful in this setting. It mixes the two colors according to the particular transition composition and adds an explaining gradient bar:

    transitionPlot(trn_mtrx_3D,
                   fill_start_box = c("#5C246E", "#00688B"),
                   type_of_arrow = "gradient")

Mixed text colors can be useful when one background color is brighter and white text becomes unreadable:

    transitionPlot(trn_mtrx_3D,
                   txt_start_clr = c("white", "black"),
                   fill_start_box = c("#5C246E", "#BFEFFF"),
                   type_of_arrow = "gradient")