# Plotting trait data

Many packages exist to visualize trait data for biological species. deeptime similarly has a few novel ways to help you plot your data in useful ways. We’ll first load some packages and example data so we can demonstrate some of this functionality.

    # Load deeptime
    library(deeptime)
    # Load other packages
    library(ggplot2)
    library(dplyr)
    # Load dispRity for example data
    library(dispRity)
    data(demo_data)
    # Load paleotree for example data
    library(phytools)
    data(mammal.tree)
    data(mammal.data)

## Plot disparity through time

A common way to visualize trait data, especially for fossil species, is to show the two-dimensional trait distribution for several time intervals. This allows the viewer to easily compare the trait distribution through time. However, producing such a plot has historically been very time intensive, often involving the use of custom code and image editing software (e.g., Inkscape). While a single function to accomplish such a visualization still does not exist for `{ggplot2}` (yet…), the `coord_trans_xy()` function can be used to generate a similar plot with sheared trait space across several time intervals.

    # make transformer
    library(ggforce)
    trans <- linear_trans(shear(.75, 0))

    # prepare data to be plotted
    crinoids <- as.data.frame(demo_data$wright$matrix[[1]][, 1:2])
    crinoids$time <- "before extinction"
    crinoids$time[demo_data$wright$subsets$after$elements] <- "after extinction"

    # a box to outline the trait space
    square <- data.frame(V1 = c(-.6, -.6, .6, .6), V2 = c(-.4, .4, .4, -.4))

    ggplot() +
      geom_segment(
        data = data.frame(
          x = -.6, y = seq(-.4, .4, .2),
          xend = .6, yend = seq(-0.4, .4, .2)
        ),
        aes(x = x, y = y, xend = xend, yend = yend),
        linetype = "dashed", color = "grey"
      ) +
      geom_segment(
        data = data.frame(
          x = seq(-.6, .6, .2), y = -.4,
          xend = seq(-.6, .6, .2), yend = .4
        ),
        aes(x = x, y = y, xend = xend, yend = yend),
        linetype = "dashed", color = "grey"
      ) +
      geom_polygon(data = square, aes(x = V1, y = V2), fill = NA, color = "black") +
      geom_point(data = crinoids, aes(x = V1, y = V2), color = "black") +
      coord_trans_xy(trans = trans, expand = FALSE) +
      labs(x = "PCO1", y = "PCO2") +
      theme_classic() +
      facet_wrap(~time, ncol = 1, strip.position = "right") +
      theme(panel.spacing = unit(1, "lines"), panel.background = element_blank())

### Disparity in base R

The `disparity_through_time()` function accomplishes nearly all of the work for you if you are comfortable plotting within the `{lattice}` framework (base R). Note that it may take some tweaking (especially the `aspect` argument) to get the results to look the way you want.

    crinoids$time <- factor(crinoids$time)
    disparity_through_time(time ~ V2 * V1,
      data = crinoids, groups = time, aspect = c(1.5, .6),
      xlim = c(-.6, .6), ylim = c(-.5, .5),
      col.regions = "lightyellow", col.point = c("red", "blue"),
      par.settings = list(
        axis.line = list(col = "transparent"),
        layout.heights =
          list(
            top.padding = -20, main.key.padding = 0,
            key.axis.padding = 0, axis.xlab.padding = 0,
            xlab.key.padding = 0, key.sub.padding = 0,
            bottom.padding = -20
          ),
        layout.widths =
          list(
            left.padding = -10, key.ylab.padding = 0,
            ylab.axis.padding = 0, axis.key.padding = 0,
            right.padding = 0
          )
      )
    )
    ## Warning: `disparity_through_time()` was deprecated in deeptime 2.4.0.
    ## This warning is displayed once per session.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    ## generated.

## Phylomorphospaces

Often, trait data will be accompanied with a phylogeny. You may want to visualize both your phylogeny, the traits of your species, and the evolution of the trait along your phylogeny. To accomplish this, you can create a two-dimensional phylomorphospace. The `{phytools}` package has the `phytools::phylomorphospace()` function for accomplishing this in base R. The `geom_phylomorpho()` function in deeptime will help you accomplish this with `ggplot()`. Note that labels can be added using `geom_label()` or `ggrepel::geom_label_repel()`, but they are not demonstrated here because they would obscure the phylogenetic relationships.

    mammal.data$label <- rownames(mammal.data)

    ggplot(mammal.data, aes(x = bodyMass, y = homeRange, label = label)) +
      geom_phylomorpho(mammal.tree) +
      theme_classic()