In PsyTeachR/reprores-v2: Data Skills for Reproducible Research

# please do not alter this code chunk
knitr::opts_chunk$set(echo = FALSE, 
                      warning = FALSE,
                      message = FALSE, 
                      error = TRUE)
library(tidyverse)
library(patchwork)
library(reprores)

# install the class package reprores to access built-in data
# devtools::install_github("psyteachr/reprores-v2)
# or download data from the website
# https://psyteachr.github.io/reprores/data/data.zip

Generate the plots below showing the distribution of dog weight by breed.

# do not edit this chunk
# dog weights estimated from http://petobesityprevention.org/ideal-weight-ranges/

set.seed(0) # makes sure random numbers are reproducible

dogs <- tibble(
  breed = rep(c("beagle", "boxer", "bulldog"), each = 100),
  weight = c(
    rnorm(100, 24, 6),
    rnorm(100, 62.5, 12.5),
    rnorm(100, 45, 5)
  )
)

Violin Plot

Make a violin plot with breed on the x-axis and weight on the y-axis. Make each breed white, 50% transparent, and outlined in a different colour, but omit the legend.

dog_violin <- ggplot(dogs, aes(breed, weight, colour = breed)) +
  geom_violin(fill = "white", alpha = .5, show.legend = FALSE)

dog_violin # prints the plot below

Boxplot

Make a boxplot with breed on the x-axis and weight on the y-axis. Make each breed white, 50% transparent, and outlined in a different colour, but omit the legend.

dog_boxplot <- ggplot(dogs, aes(breed, weight, colour = breed)) +
  geom_boxplot(fill = "white", alpha = .5, show.legend = FALSE)

dog_boxplot # prints the plot below

Density plot

Make a density plot with weight on the x-axis. Make each breed white, 50% transparent, and outlined in a different colour, but omit the legend.

dog_density <- ggplot(dogs, aes(weight, colour = breed)) +
  geom_density(fill = "white", alpha = .5, show.legend = FALSE)

dog_density # prints the plot below

Column Plot

Use stat_summary to create a column plot with breed on the x-axis and weight on the y-axis and error bars showing 1 standard error. Make each breed white, 50% transparent, and outlined in a different colour, but have the error bars be black. Omit the legend.

dog_column <- ggplot(dogs, aes(breed, weight, colour = breed)) +
  stat_summary(geom = "col", fill = "white", alpha = .5) +
  stat_summary(geom = "errorbar", width = 0, colour = "black") +
  theme(legend.position = "none")

dog_column # prints the plot below

Grid

Create a grid of the violin plot, boxplot, and column plot above with all three plots on the same row. Make the figure 8 inches wide, 4 inches tall, and the image cover 100% of the width of the markdown output.

dog_violin + dog_boxplot + dog_column +
  patchwork::plot_layout(nrow = 1)

Changing defaults

For the four plots above, change the axis labels so the x-axis reads "Breed of Dog" or "Weight of Dog" (depending on the plot type) and the y-axis reads "Weight of Dog", "Number of Dogs", or "Density of Dogs" (depending on the plot type).

Change the default colours to "orange", "dodgerblue", and "hotpink".

Add a title to each plot describing the plot type.

Save each plot as a PNG file with the names "dog_violin.png", "dog_boxplot.png", "dog_density.png", and "dog_column.png" (the names are important so they show up in the code below).

# Hint: you can add changes to an existing plot, e.g.:
# dog_density + xlim(0, 100)

colours <- scale_colour_manual(values = c("orange", "dodgerblue", "hotpink"))
labs <- labs(x = "Breed of Dog", y = "Weight of Dog")

v <- dog_violin + colours + labs +
  ggtitle("Violin Plot")
ggsave("dog_violin.png")

b <- dog_boxplot + colours + labs +
  ggtitle("Box Plot")
ggsave("dog_boxplot.png")

d <- dog_density + colours +
  labs(title = "Density Plot",
       x = "Weight of Dog",
       y = "Density of Dogs")
ggsave("dog_density.png")

c <- dog_column + colours + labs +
  ggtitle("Column Plot")
ggsave("dog_column.png")

# do not change; displays the images saved above
knitr::include_graphics("dog_violin.png")
knitr::include_graphics("dog_boxplot.png")
knitr::include_graphics("dog_density.png")
knitr::include_graphics("dog_column.png")

Line plot

Represent the relationships among disgust subscales from the dataset reprores::disgust_scores.

Graph the linear relationship between moral and pathogen disgust. Make sure the axes run from the minimum to maximum possible scores on both axes. Give the graph an appropriate title and axis labels.

data("disgust_scores", package = "reprores")

disgust_lineplot <- ggplot(disgust_scores, aes(moral, pathogen)) +
  geom_smooth(formula = y~x, method = lm)

disgust_lineplot # prints the plot below

2D Density plot

If you add geom_point() to the plot above, you'll see that there is too much data for this visualisation to make sense. Instead, create a 2d density plot of the relationship between moral and pathogen disgust for disgust_scores.

disgust_density <- ggplot(disgust_scores, aes(moral, pathogen)) +
  geom_density2d_filled()

disgust_density # prints the plot below

Many correlated variables

Create a heatmap of the relationships among all the questions in reprores::disgust_cors. The correlations have already been calculated for you.

Bonus: Figure out how to rotate the text on the x-axis so it's readable.

data("disgust_cors", package = "reprores")

disgust_heatmap <- ggplot(disgust_cors, aes(V1, V2, fill = r)) +
  geom_tile() +
  scale_fill_viridis_c() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

disgust_heatmap # prints the plot below

Facets

Create a grid of plots for the reprores::stroop dataset using faceting.

Plot rt for each combination of word and ink to make a 5x5 grid of density plots. Make each plot line the same colour as the ink. For bonus points, make the lines for plots where the ink colour matches the word colour thicker than the other lines.

data("stroop", package = "reprores")

word_by_ink <- ggplot(stroop, aes(rt, colour = ink, 
                      size = ink == word)) +
  geom_density(show.legend = FALSE) +
  facet_grid(word~ink, labeller = label_both) +
  # sets the colour palette to custom values
  scale_colour_manual(values = c("blue", "brown","green", "purple", "red")) +
  # you may have chosen different sizes for line thickness
  scale_size_manual(values = c(.5, 1.5))

word_by_ink # prints the plot below

Advanced Grid

Create a 3x3 grid of linear line plots from disgust_scores with columns representing the x-axis and rows representing the y-axis and assign it to disgust_grid. Put a density plot of each variable along the diagonal. Make sure the graphs have appropriate titles and axis labels and that the range of the axes are the same in all graphs.

| | moral | sexual | pathogen | |--------------|---------|---------|----------| | moral | density | line | line | | sexual | line | density | line | | pathogen | line | line | density |

# Hint: set up your 9 separate plots first

my_geom <- geom_smooth(formula = y~x, method = lm)

# regression line plots
moral_sexual <- ggplot(disgust_scores, aes(moral, sexual, color)) +
  ggtitle("Moral vs Sexual") + my_geom + xlim(0, 6) + ylim(0, 6)

moral_pathogen <- ggplot(disgust_scores, aes(moral, pathogen)) +
  ggtitle("Moral vs Pathogen") + my_geom + xlim(0, 6) + ylim(0, 6)

pathogen_moral <- ggplot(disgust_scores, aes(pathogen, moral)) +
  ggtitle("Pathogen vs Moral") + my_geom + xlim(0, 6) + ylim(0, 6)

pathogen_sexual <- ggplot(disgust_scores, aes(pathogen, sexual)) +
  ggtitle("Pathogen vs Sexual") + my_geom + xlim(0, 6) + ylim(0, 6)

sexual_moral <- ggplot(disgust_scores, aes(sexual, moral)) +
  ggtitle("Sexual vs Moral") + my_geom + xlim(0, 6) + ylim(0, 6)

sexual_pathogen <- ggplot(disgust_scores, aes(sexual, pathogen)) +
  ggtitle("Sexual vs Pathogen") + my_geom + xlim(0, 6) + ylim(0, 6)

# density plots
moral_moral <- ggplot(disgust_scores, aes(moral)) +
  geom_density() + ggtitle("Moral Disgust") + 
  xlim(0, 6) + ylim(0, 0.4)

sexual_sexual <- ggplot(disgust_scores, aes(sexual)) +
  geom_density() + ggtitle("Sexual Disgust") + 
  xlim(0, 6) + ylim(0, 0.4)

pathogen_pathogen <- ggplot(disgust_scores, aes(pathogen)) +
  geom_density() + ggtitle("Pathogen Disgust") + 
  xlim(0, 6) + ylim(0, 0.4)

# add the plots together
moral_moral + sexual_moral + pathogen_moral +
  moral_sexual + sexual_sexual + pathogen_sexual + 
  moral_pathogen + sexual_pathogen + pathogen_pathogen +
  patchwork::plot_layout(ncol = 3) +
  patchwork::plot_annotation(tag_levels = "A")

PsyTeachR/reprores-v2 documentation built on Sept. 26, 2022, 10:06 a.m.