Plotting the data
It is often desirable to visualize the preprocessed data, either as a grand average or by condition. In some cases it is even necessary to visualize the trend in the data over a continuous predictor. So, the functions ppl_plot_avg and ppl_plot_avg_contour provide straightforward plotting options for such cases. These functions internally calculate the average(s) and plot the results. The plotting is powered by ggplot2, so further customization (plot titles, custom themes, etc.) is still possible. For more information about ggplot2, please refer to its reference manual and extensive documentation.
Averaged data
Using the function ppl_plot_avg, it is possible to plot the overall average of the data. In Column simply put the column containing the pupil size data
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE) 
To add a title to the plot, simply add the title function from ggplot2.
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE) +
ggtitle("Averaged Data")
To customize the appearance of a plot (e.g., font, size, color, margins, etc.), the PupilPreTheme parameter can be set to FALSE, which reverts to the default theming in gglpot2. In this way, the user can apply a custom theme to the plot. Detailed information about creating themes can be found at ggplot2 Theme Vignette. For the purpose of illustration, the default ggplot2 theme has been applied, with the axis text elements increased in size.
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA, Cond2Labels = NA,
ErrorBar = TRUE, PupilPreTheme = FALSE) +
theme(axis.text = element_text(size = 15))
Conditional averages
The function ppl_plot_avg can also be used to plot averages for different conditions, based on a factor variable in the data. If the current factor level labels are not suitable for plotting, specify new labels using a list in Cond1Labels. This will add curves for all levels in a single plot.
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = "talker", Condition2 = NULL,
Cond1Labels = c(CH1 = "Chinese 1", CH8 = "Chinese 3",
CH9 = "Chinese 2", CH2 = "Chinese 4", EN3 = "English 1"),
Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE)
For a 2x2 design, it is possible to specify both conditions. This will create the interaction of the two conditions and plot all combinations in a single plot
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = "talker", Condition2 = "ExpLev",
Cond1Labels = c(CH1 = "Chinese 1", CH8 = "Chinese 3",
CH9 = "Chinese 2", CH2 = "Chinese 4", EN3 = "English 1"),
Cond2Labels = c(H = "High Exp", L = "Low Exp"),
ErrorBar = TRUE, PupilPreTheme = TRUE)
Error bars and Error bands
Error around the means can be plotted in two ways, either as error bars or as error bands. Note that with the included theme, the colors and shapes change for error bands to maximize readablity.
gridExtra::grid.arrange(
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE),
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = FALSE,
ErrorBand = TRUE, PupilPreTheme = TRUE),
nrow=2, ncol=1)
Confidence intervals (pointwise/simultaneous)
Rather than having standard error plotted, it is possible to have confidence intervals added to the graph. Confidence intervals can be plotted either as bars or bands and controlled using ErrorType and ConfLev. ErrorType should be set to “CI” for confidence intervals, and ConfLev set to the desired levels of confidence (by default 95). An important option is the type of desired interval, either pointwise or simultaneous, using CItype. Pointwise CIs use the confidence level provided for each interval plotted. Simultaneous CIs are, on the other hand, corrected for multiple intervals using the Bonferroni method. Underlyingly this correction is done using the number of data points along the x-axis (Time).
gridExtra::grid.arrange(
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = FALSE, ErrorBand = TRUE,
ErrorType = "CI", ConfLev = 95, CItype = "pointwise",
PupilPreTheme = TRUE),
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, ErrorBar = FALSE, ErrorBand = TRUE,
ErrorType = "CI", ConfLev = 95, CItype = "simultaneous",
PupilPreTheme = TRUE),
nrow=2, ncol=1)## Grand average calculated using Event means.## Plot created with pointwise confindence intervals (set to 95%).## Grand average calculated using Event means.## Plot created with simultaneous confindence intervals (adjusted to 99.95% using the Bonferroni method).
Calculation of averages - Mean vs. Grand mean
By default, the plotting function calculates the overall mean in the data set by time. However, by changing the input to the parameter Averaging, it is possible to supply a column name for which grand mean (mean of means) can be calculated (e.g., “Subject”). Note that for balanced data, the resultant mean will be the same, but the size of the error bars/bands will change. For example, given the small number of participants in this data set, the error bars become much wider.
ppl_plot_avg(data = dat, xlim = c(0, 2000), Column = "Pupil",
Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA,
Cond2Labels = NA, Averaging = "Subject", ErrorBar = TRUE,
ErrorType = "SE", PupilPreTheme = TRUE) 
Difference plots
The function ppl_plot_avg_cdiff can also be used to plot the average difference between two conditions.
ppl_plot_avg_cdiff(data = dat, Column = "Pupil",
Condition = list(talker = c("EN3", "CH1")),
ErrorBar = TRUE, PupilPreTheme = TRUE)
Error bands and confidence intervals (both pointwise and simultaneous) work the same way as in the ppl_plot_avg function. With regard to averaging, please note that the function will check that both levels of the condition occur for each level of the column provided in Averaging (e.g., Subject or Item), as this is necessary to calculate the difference based on subject or item means. If this is not the case, the function will stop. If you would still like to produce the plot based on the difference between sample means of the levels, you can set Averaging = NULL.
Conditional contour surface
In some cases, studies have not employed a factorial design; rather they aim to investigate continuous variables. Therefore, using the function ppl_plot_avg_contour it is also possible to create a contour plot representing the looks to one interest area as a surface over the continuous variable and Time. This function calculates the average time series at each value of the continuous variable and applies a smooth (utilizing the function gam in the package mgcv) over the surface. The function then plots the result as a contour plot. Here, the example plots pupil dilation as a function of Trial and Time.
ppl_plot_avg_contour(data = dat, Column = "Pupil", Var = "TRIAL_INDEX",
VarLabel = "Trial", xlim = c(0,2000), PupilPreTheme = TRUE,
Colors = c("gray20", "gray90"))
It is possible to change the contour colors and add a title. ggplot2 accepts predefined palette colors, RGB, hexadecimal, among others.
ppl_plot_avg_contour(data = dat, Column = "Pupil", Var = "TRIAL_INDEX",
VarLabel = "Trial", xlim = c(0,2000), PupilPreTheme = TRUE,
Colors = c("red", "green")) + ggtitle("Pupil dilation")
Averaging works the same way as in the ppl_plot_avg function.
