Customizing superb plots

# Customizing `superb` plots

Creating a plot involves reading raw data and compiling these into summary statistics. This step is handled by `superb` transparently. The second, more involving step, however is to customize the plots so that it looks appealing to the readers.

In this vignette, we go rapidly over `superb` functionalities. Instead, we provide worked-out examples producing fully customized plots. We proceed with examples taken from scientific articles. The first example produces a rain-drop plot, the second a bar plot whose origin is not zero.

In the following, we need the following libraries:

    ## Load relevant packages
    library(superb)             # for superbPlot
    library(ggplot2)            # for all the graphic directives
    library(gridExtra)          # for grid.arrange

If they are not present on your computer, first upload them to your computer with `install.packages("name of the package")`.

# Figure 2 of Hofer, Langmann, Burkart and Neubauer, 2022.

In their study, Hofer, Langmann, Burkart, & Neubauer (2022) examined who is the best judges of one’s abilities. Examining self-ratings vs. other-ratings in six domain, they found out that we are not always the best judges. They present in their Figure 2 a rain-cloud plot (Allen, Poggiali, Whitaker, Marshall, & Kievit (2019)) illustrating the ratings.

In what follow, we discuss how this plot could be customized after its initial creation with `superb`.

As the six domains are within-subject ratings, the data must be composed of 6 columns (at least, there can be additional columns; they won’t be illustrated herein). In case you do not have such data, the following subsection generates mock data.

## Generating mock data

We generate two sets of mock data from six sets of means and standard deviations:

    Astats <- data.frame(
        MNs = c(6.75, 6.00, 5.50, 6.50, 8.00, 8.75),
        SDs = c(2.00, 3.00, 3.50, 3.50, 1.25, 1.25)
    )
    dtaA <- apply(Astats, 1,
        function(stat) {rnorm(100, mean=stat[1], sd=stat[2])}
    )
    dtaA <- data.frame(dtaA)
    colnames(dtaA) <- c("Verbal", "Numerical", "Spatial", "Creativity", "Intrapersonal", "Interpersonal")

    Bstats <- data.frame(
        MNs = c(3.33, 3.00, 2.50, 3.00, 2.75, 3.50),
        SDs = c(0.25, 0.50, 0.66, 0.50, 0.25, 0.25)
    )
    dtaB <- apply(Bstats, 1,
        function(stat) {rnorm(100, mean=stat[1], sd=stat[2])}
    )
    dtaB <- data.frame(dtaB)
    colnames(dtaB) <- c("Verbal", "Numerical", "Spatial", "Creativity", "Intrapersonal", "Interpersonal")

The datasets are `data.frame`s called `dtaA` and `dtaB`. Their columns names are the dependent variables, e.g., “Verbal”, “Numerical”, “Spatial”, “Creativity”, “Intrapersonal”, “Interpersonal”.

## Making the top-row plot

For convenience, we make lists of the desired colors and labels we want to appear on the x-axis:

    mycolors <- c("seagreen","chocolate2","mediumpurple3","deeppink","chartreuse4", "darkgoldenrod1")
    mylabels <- c("Verbal", "Numerical", "Spatial", "Creativity", "Intrapersonal", "Interpersonal")

We are ready to make the plot with the desired adjustments:

    pltA <- superb(
        crange(Verbal, Interpersonal) ~ ., # no between-subject factors
        dtaA,                       # plot for the first data set...
        WSFactors   = "Domain(6)",  # ...a within-subject design with 6 levels
        adjustments = list(
            purpose = "difference", # we want to compare means
            decorrelation = "CM"    # and error bars are correlated-adjusted
        ),
        plotLayout  = "raincloud",

        # the following (optional) arguments are adjusting some of the visuals
        pointParams    = list(size = 0.75),
        jitterParams   = list(width =0.1, shape=21,size=0.05,alpha=1), # less dispersed jitter dots,
        violinParams   = list(trim=TRUE, alpha=1),                     # not transparent,
        errorbarParams = list(width = 0.1, linewidth=0.5)              # wider bars, thicker lines.
    )
    pltA

Figure 2, preliminary version

As seen, this plot is a standard, colorless, plot. It contains all that is needed; it is just plain drab and the labels are generic ones (on the vertical axis and on the horizontal axis).

## Adding a color layer to the plot

Using `superb`, if there is only one factor, superb will consider that it is the one on the x-axis and there is therefore no other layers in the plot. This is why the current plot is colorless.

It is possible, post-hoc, to indicate that we wish additional layers in the plot.

In the present, we want to add the `fill` and the `color` of dots layers. These layers are to be “connected” to the sole factor in the present example (that is, `Domain`). Consequently, the x-axis labels, the fill color and the dot color are all redondant information identifying the condition.

To do this, simply add an aesthetic graphic directive to `pltA` with:

    pltA + aes(fill = factor(Domain), colour = factor(Domain))

Figure 2, version with colors

## Adding graphic directives for fine-tuning the plot

We can customize any `superb` plot by adding graphic directives one-by-one using the operator `+`, or we can collect all the directives in a list, and add this list once. As we have two plots with mostly the same directives, we use this second approach.

Typically, a plot is customized by picking a theme. The default `theme_bw()` is grayish, so we move to `theme_classic()`. We also customize specific aspects of this theme with `theme()` directives.

These changes are all collected within the list `commonstyle` below:

    commonstyle <- list(
        theme_classic(),                             # It has no background, no bounding box.

        # We customize this theme further:
        theme(axis.line=element_line(linewidth=0.50), # We make the axes thicker...
            axis.text = element_text(size = 10),      # their text bigger...
            axis.title = element_text(size = 12),     # their labels bigger...
            plot.title = element_text(size = 10),     # and the title bigger as well.
            panel.grid = element_blank(),             # We remove the grid lines
            legend.position = "none"                  # ... and we hide the side legend.
        ),

        # Finally, we place tick marks on the units
        scale_y_continuous( breaks=1:10 ),

        # set the labels to be displayed
        scale_x_discrete(name="Domain", labels = mylabels),

        # and set colours to both colour and fill layers
        scale_discrete_manual(aesthetic =c("fill","colour"), values = mycolors)
    )

We also changed the vertical scale (tick marks at designated positions) and the horizontal scale with names on the tick marks (sadly, `superb` replaces them with consecutive numbers…) and colors to fill the clouds (`fill`) and their borders (`colour`) as well as the rain drop colors.

Examining this plot with the `commonstyle` added, we get

    finalpltA <- pltA + aes(fill = factor(Domain), colour = factor(Domain)) +
        commonstyle +                           # all the above directive are added;
        coord_cartesian( ylim = c(1,10) ) +     # the y-axis bounds are given ;
        labs(title="A") +                       # the plot is labeled "A"...
        ylab("Self-worth relevance")            # and the y-axis label given.
    finalpltA

Figure 2, final version

## Making the second row of the figure

We do exactly the same for the second plot. We just change the data set to `dtaB` and in the last graphic directives, using options tailored specifically to this second data set (smaller y-axis range, different label, etc.):

    pltB <- superb(
        crange(Verbal, Interpersonal) ~ ., # no between-subject factors
        dtaB,                       # the second data set...
        WSFactors = "Domain(6)",    # ...a within-subject design with 6 levels
        adjustments = list(
            purpose = "difference", # we want to compare means
            decorrelation = "CM"    # and error bars are correlated-adjusted
        ),
        plotLayout   = "raincloud",
        # the following (optional) arguments are adjusting some of the visuals
        pointParams  = list(size = 0.75),
        jitterParams = list(width =0.1, shape=21,size=0.05,alpha=1), # less dispersed jitter dots,
        violinParams = list(trim=TRUE, alpha=1,adjust=3),            # not semi-transparent, smoother
        errorbarParams = list(width = 0.1, linewidth=0.5)                 # wider bars, thicker lines.
    )
    finalpltB <- pltB + aes(fill = factor(Domain), colour = factor(Domain)) +
        commonstyle +                           # the following three lines are the differences:
        coord_cartesian( ylim = c(1,5) ) +      # the limits, 1 to 5, are different
        labs(title="B") +                       # the plot is differently-labeled
        ylab("Judgment certainty")              # and the y-axis label differns.
    finalpltB

Figure 2, bottom row

## Combining and saving both plots

Finally, we assemble the two plots together

    finalplt <- grid.arrange(finalpltA, finalpltB, ncol=1)

Figure 2, final version

It can be saved with high-resolution if desired with

    ggsave( "Figure2.png",
        plot=finalplt,
        device = "png",
        dpi = 320,          # pixels per inche
        units = "cm",       # or "in" for dimensions in inches
        width = 17,         # as found in the article
        height = 13
    )

That’s it!

# Figure 2 of Ma and Abrams, 2023.

In their study, Ma & Abrams (2023) examined whether participants can suppress attentional deployment under unpredictable visual distractor attributes. They found for the first time that observers can indeed suppress salient, unique colored, distractors even if the color was not known before hand.

To proceed, first get to the authors’ OSF https://osf.io/r52db and follow the instructions to obtain the dataframe `cleandata`.

Because response times (RTs) were recorded in second, we convert them to milisecond:

    cleandata$absentrt = cleandata$absentrt*1000
    cleandata$presentrt = cleandata$presentrt*1000

As a check, here is the first six lines of that data frame:

    head(cleandata)

    ##   subject absentrt presentrt absentacc presentacc
    ## 1     201 906.9648  880.5836  0.984375  0.9843750
    ## 2     202 750.1645  722.7798  0.937500  0.9921875
    ## 3     203 814.3321  717.3632  0.953125  0.9765625
    ## 4     204 985.0208  908.4251  0.984375  0.9921875
    ## 5     205 927.9098  859.6929  0.875000  0.9375000
    ## 6     206 962.0722  848.8763  0.859375  0.9140625

Please select the colors desired for the bars:

    mycolors = c("black","lightgray")

In addition to the above libraries, we also need the `scales` library so that we can modify the vertical axis of the plot. Indeed, bar charts by default start at zero, but for the present data (response times and mean accuracies), a scales which does not start from zero is more appropriate. We then create a shift transformation function with a non-zero start \(d\):

    library(scales)     # for a translated scale using trans_new()

    shift_trans = function(d = 0) {
      scales::trans_new("shift", transform = function(x) x - d, inverse = function(y) y + d)
    }

We’re all set! We are ready to make the first plot, here RTs, as a function of the presence or absence of the colored distractor. Because (a) we want to compare the bars, we use difference-adjusted confidence intervals; (b) the data were collected in a within-subject design, we use a correlation-adjusted confidence intervals.

    # defaults are means with 95% confidence intervals, so not specified
    pltA <- superbPlot( cleandata,
        WSFactors = "target(2)",
        variables = c("absentrt", "presentrt"),
        adjustments = list(
            purpose = "difference",
            decorrelation = "CM"),
        plotLayout  = "bar",
        errorbarParams = list(colour = "gray35", width = 0.05)
    )

    ## superb::FYI: The HyunhFeldtEpsilon measure of sphericity per group are  1.000

    pltA

Figure 1, preliminary version

As this is the default, the vertical axis starts at zero. Let’s add the `shift_trans` scale, limit the range to 720-900, and show breaks on every 20 units:

    # attached the shifted scale to it
    pltA <- pltA + scale_y_continuous(
        trans = shift_trans(720),      # use translated bars
        limits = c(720,919),           # limit the plot range
        breaks = seq(720,900,20),      # define major ticks
        expand = c(0,0) )              # no expansions over the plotting area
    pltA

Figure 2, version with adequate vertical scale

We can do better: changing the default fonts, remove the legend, etc. We store these graphic directives in a list because the same are used for the accuracy plot:

    ornaments <- list(
        theme_classic(base_size = 14) + theme( legend.position = "none" ),
        aes(width = 0.5, fill = factor(target), colour = factor(target) ),
        scale_discrete_manual(aesthetic =c("fill","colour"), values = mycolors),
        scale_x_discrete(name="Color Singleton\nDistractor", labels = c("Absent","Present"))
    )
    pltA <- pltA + ornaments + ylab("Reaction time (ms)")
    pltA

Figure 3, version with theme and details adjusted

Finally, we put an indication regarding the significant result:

    pltA <- pltA + showSignificance( c(1,2), 870, -8,
        "Singleton presence\nbenefit, p < .001",
        segmentParams = list(linewidth = 1))

    # this is it! Check the result
    pltA

Figure 4, final version for RTs

No need to go over all the details for the mean accuracy plot. We do all the steps in a single command:

    pltB <- superbPlot( cleandata,
        WSFactors = "target(2)",
        variables = c("absentacc", "presentacc"),
        adjustments = list(
            purpose = "difference",
            decorrelation = "CM"),
        plotLayout  = "bar",
        errorbarParams = list(colour = "gray35", width = 0.05)
    ) +
    scale_y_continuous(
        trans = shift_trans(0.9),           # use translated bars
        limits = c(0.9, 1.0),               # limit the plot range
        breaks = seq(0.90, 1.00, 0.01),     # define major ticks
        expand = c(0,0) ) +                 # remove empty space around plotting surface
    ornaments +
    ylab("Accuracy (proportion correct)") +
    showSignificance( c(1,2), 0.985, -0.005,
        "Singleton presence\nbenefit, p = .010",
        segmentParams = list(linewidth = 1) )

    ## superb::FYI: The HyunhFeldtEpsilon measure of sphericity per group are  1.000

    ## superb::FYI: All the groups' data are compound symmetric. Consider using CA or UA.

    # this is it! Check the result
    pltB

Figure 5, final version for mean accuracies

Put the two plots side-by-side and save your work!

    finalplt <- grid.arrange(pltA, pltB, ncol=2)

Figure 6, final version

    #ggsave( "Figure2b.png",
    #    plot=finalplt,
    #    device = "png",
    #    dpi = 320,          # pixels per inche
    #    units = "cm",       # or "in" for dimensions in inches
    #    width = 20,         # as found in the article
    #    height = 15
    #)

Regarding the information provided by `superb`:

    ## superb::FYI: The HyunhFeldtEpsilon measure of sphericity per group are  1.000
    ## superb::FYI: All the groups' data are compound symmetric. Consider using CA.

note that with only two repeated measures, sphericity is always met (Epsilon = 1.00) so nothing to do with this comment. Compound symmetry is a weaker form of the sphericity assumption. When compound symmetry is met, you can decorrelate the data using either `CM` or `CA`. You won’t see much differences between the two techniques, so you may as well ignore this comment.

Enjoy!

# References

Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R., & Kievit, R. A. (2019). Raincloud plots: A multi-platform tool for robust data visualization. Wellcome Open Research, 4.
Hofer, G., Langmann, L., Burkart, R., & Neubauer, A. C. (2022). Who knows what we are good at? Unique insights of the self, knowledgeable informants, and strangers into a person’s abilities. Journal of Research in Personality, 104226. https://doi.org/10.1016/j.jrp.2022.104226
Ma, X., & Abrams, R. A. (2023). Ignoring the unknown: Attentional suppression of unpredictable visual distraction. Journal of Experimental Psychology: Human Perception and Performance, 49, 1–6. https://doi.org/10.1037/xhp0001067