Hello fellow R pirates! For those of you who didn’t see it, I recentlywrote a post demonstrating the pirateplot() function in the yarrr package. The pirateplot() function replaces deceptive (and boring) bar plots with a full RDI plot, capable of plotting Raw data (and smoothed densities), Descriptive statistics (like means and medians), and Inferential statistics (a 95% Bayesian Highest Density Interval “HDI”).
In the past 48 hours I’ve had an overwhelmingly positive response to the pirateplot() function. At the same time, I received several great recommendations for tweaks and improvements to the function to make it even better. After consulting the original pirate text for the function, I decided that the changes stay true to the original piratery intent of the pirate plot. I’m sure the founding members of the pirate plot would be proud.
Let’s go over the changes! To use the latest version of the pirateplot() function, be sure to install the latest version of the yarrr package:
# install.packages("devtools") # Only if you don't have the devtools library already installed library("devtools") install_github("ndphillips/yarrr")
Once you’ve installed the latest version, load the package with library()
Now you’re ready to make some pirate plots! Here are the major updates to the function:
The biggest updated to pirateplot() is the addition of opacity themes which are designated by a new argument called theme.o. The input to this argument defines an opacity theme for the entire plot. Themes 1, 2, and 3 create specific values of the element opacities (the bars, beans, points, hdis, and lines), while Theme 0 sets all opacities to 0. Thankfully, the themes just set default values for the individual element opacities — you can still override the opacities of any specific object by including an object specific opacity value.
Here are examples of the three different themes applied to the ChickWeight dataset:
Theme 1 emphasises the bar with light points and beans (I’ll use the appletv palette for this one)
pirateplot(formula = weight ~ Diet, data = ChickWeight, main = "Theme 1/nappletv palette", theme.o = 1, pal = "appletv")
Theme 2 emphasises the points and beans (using the southpark palette)
pirateplot(formula = weight ~ Diet, data = ChickWeight, main = "Theme 2/nsouthpark palette", theme.o = 2, pal = "southpark")
Theme 3 Emphases the 95% Highest Density Intervals (HDIs). Keep in mind that calculating HDIs can take a few seconds for each bean… Here I’ll use the Basel palette.
pirateplot(formula = weight ~ Diet, data = ChickWeight, main = "Theme 3/nbasel palette", theme.o = 3, pal = "basel")
In Theme 0, all opacities are set to 0 by default, so you can just individually specify the opacity of each element. In this example, I’ll turn the lines on full-blast, and turn the points on slighly. I’ll also increase the amount of jittering and size of the points. I’ll also use the google palette.
pirateplot(formula = weight ~ Diet, data = ChickWeight, main = "Theme 0/ngoogle palette", pal = "google", point.o = .2, line.o = 1, theme.o = 0, line.lwd = 10, point.pch = 16, point.cex = 1.5, jitter.val = .1)
Of course, you can still change the colors of the plotting elements with the par argument, and the background using the back.col argument. Here’s an x-ray version of Theme 3
pirateplot(formula = weight ~ Diet, data = ChickWeight, main = "Theme 3/nlight color with black background", pal = "white", theme.o = 3, point.pch = 16, back.col = gray(.2))
You can now include gridlines in your plot with the gl.col argument. Just specify the color of the lines and the function will put them in reasonable places. The following plot also shows how pirateplot() handles two independent variables:
pirateplot(formula = weight ~ Diet + Time, data = subset(ChickWeight, Time < 10), theme.o = 2, pal = "basel", point.pch = 16, gl.col = gray(.8), main = "Two IVs/nWith gridlines")
Other minor changes
I’ve also made the following smaller changes
- The function no longer automatically sorts the levels of the IV. It will plot levels of the IV(s) in the order the are found in the original dataframe.
- You can now manually change the color of the bar borders with the bar.border.col argument.
Happy pirate plotting!
As always, I am very happy to receive more comments and feedback on the function. You can write me at firstname.lastname@example.org. Happy pirate plotting!
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