Re-creating plots to learn cool tricks and practice problem-solving.
library(cowplot)
library(glue)
library(ggtext)
library(gridtext)
library(here)
library(magick)
library(RColorBrewer)
library(tidyverse)
set.seed(2020)View the plots below and try to write the code that creates them! There are more exercises here than you can probably get to in the time allotted. Feel free to jump around and pick ones to work on based on how interested you are in learning how to create the plot. At the end, we’ll each share one solution.
As much as this is an exercise in data viz with R, it’s also an exercise in finding solutions in package documentation and general problem-solving. Google is your friend! If you get stuck, take a look at the hints or send Kelly a message in Slack.
Source: Claus Wilke’s talk at rstudio::conf(2020)
otu_data <- tribble(~otu, ~bact, ~value,
1, 'Staphylococceae', -0.5,
2, 'Moraxella', 0.5,
3, 'Streptococcus', 2,
4, 'Acinetobacter', 3.0
) %>% mutate(name = glue("*{bact}* (OTU {otu})"))
otu_data %>%
ggplot(aes(XXXXXX, XXXXXX)) +
geom_XXXXXX() +
XXXXXX() +
theme(axis.text.y = XXXXXX)## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
Source: Claus Wilke’s talk at rstudio::conf(2020)
# make some fake data
otu_data <- tribble(~otu, ~bact, ~value,
1, 'Staphylococceae', -0.5,
2, 'Moraxella', 0.5,
3, 'Streptococcus', 2,
4, 'Acinetobacter', 3.0
) %>%
mutate(color = brewer.pal(4, "Dark2"),
name = glue("<i style='color:{color}'>{bact}</i> (OTU {otu})")
)
# plot it
otu_data %>%
ggplot(aes(name, value, fill=color)) +
geom_XXXXXX() +
scale_XXXXXX_identity() +
XXXXXX_flip() +
XXXXXX(axis.text.y = XXXXXX)## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
Inspiration: fig. 2C from Jay’s recent journal club paper: Zhai et al 2018 Nature Med
# make some fake data
time_data <-tibble(time = seq(0,5,0.1),
yes = sin(time * 0.8) + 0.8,
no = sin(time * -0.5) + 1
) %>% pivot_longer(-time, names_to = "infected", values_to = "value")
head(time_data)## # A tibble: 6 x 3
## time infected value
## <dbl> <chr> <dbl>
## 1 0 yes 0.8
## 2 0 no 1
## 3 0.1 yes 0.880
## 4 0.1 no 0.950
## 5 0.2 yes 0.959
## 6 0.2 no 0.900
# plot it
time_data %>% ggplot(aes(x = XXXXXX, y = XXXXXX, color = infected)) +
geom_XXXXXX() +
ylab("<b style='color:#00BFC4'>Candidemia</b> vs. <b style='color:#F8766D'>no Candidemia</b> ITS1 diversity") +
theme_XXXXXX() +
theme(legend.position = XXXXXX,
axis.title.y = XXXXXX)## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
Adapted from: https://github.com/SchlossLab/compositional_data_analysis
palette = brewer.pal(n = 4, name = "Paired")
colors = c(A = palette[[2]],
B = palette[[3]])
otu_table <- tibble(
sample = c("1", "2", "3", "1", "2", "3"),
otu = c("A", "A", "A", "B", "B", "B"),
abun = c(5, 15, 6, 15, 5, 2)
) %>% mutate(color = colors[otu])
# plot total counts (aboslute abundace)
otu_table %>%
ggplot(aes(x = sample, y = XXXXXX, fill = XXXXXX)) +
geom_XXXXXX() +
scale_XXXXXX_XXXXXX() +
XXXXXX("Total bacteria") +
theme_classic()## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
Adapted from: https://github.com/SchlossLab/compositional_data_analysis
otu_table <- tibble(
sample = c("1", "2", "3", "1", "2", "3"),
otu = c("A", "A", "A", "B", "B", "B"),
abun = c(5, 15, 6, 15, 5, 2)
)
# from https://github.com/mothur/logo
logo_file <- here("figures", "mothur_RGB.png")
# plot total counts (aboslute abundace)
plot_total <- otu_table %>%
ggplot(aes(x = XXXXXX, y = XXXXXX, fill = XXXXXX)) +
geom_XXXXXX() +
XXXXXX("Total bacteria") +
theme_classic()## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
ggXXXX() +
draw_XXXXXX(plot_total) +
draw_XXXXXX(logo_file, x = 1, y = 1,
hjust = 1.2, vjust = 1.2,
width = 0.3, height = 0.3)## Error in ggXXXX(): could not find function "ggXXXX"
With great power, comes great responsibility. Use at your own risk!
Adapted from: https://wilkelab.org/cowplot/articles/drawing_with_on_plots.html#combining-plots-and-images
rides <- read_csv('https://raw.githubusercontent.com/kelly-sovacool/strava/master/data/processed/activities.csv', col_types = cols()) %>%
filter(distance_mi > 1, as.character(type) == 'Ride', year >= 2019) %>%
select(distance_mi, start_date)
# source https://www.pinclipart.com/picdir/big/196-1969309_free-bicycle-bike-cartoon-no-background-clipart.png
bike_img <- here('figures', 'bike.png') %>%
image_read() %>%
image_colorize(70, "white")
# make the plot
rides_plot <- rides %>%
ggplot(aes(XXXXXX, XXXXXX)) +
geom_point(color='blue', alpha=0.8, size=2) +
theme_XXXXXX()## Error in theme_XXXXXX(): could not find function "theme_XXXXXX"
XXXXXX() +
draw_XXXXXX(bike_img) +
draw_XXXXXX(rides_plot)## Error in XXXXXX(): could not find function "XXXXXX"
Adapted from: https://github.com/SchlossLab/OptiFitAnalysis/tree/master/exploratory/2020#performance-as-measured-by-runtime
benchmarks_fit <-read_tsv('https://raw.githubusercontent.com/SchlossLab/OptiFitAnalysis/master/subworkflows/2_fit_reference_db/results/benchmarks.tsv?token=AEHR6TPPUNNM245DZ7TUP2C7ADK5E', col_types = cols())
benchmarks_clust <- read_tsv('https://raw.githubusercontent.com/SchlossLab/OptiFitAnalysis/master/subworkflows/1_prep_samples/results/benchmarks.tsv?token=AEHR6TNCIGRVN3B5GEVRVNC7ADLAS', col_types = cols())
plot_box_time <- function(df) {
df %>%
group_by(dataset, method) %>%
ggplot(aes(x = method, y = s, color = dataset)) +
geom_XXXXXX() +
scale_XXXXXX_XXXXXX() +
facet_XXXXXX("ref") +
ylim(0,2100) +
labs(y = 'seconds') +
theme_XXXXXX() +
XXXXXX(axis.title.x = element_blank())
}
time_plot_fit <- benchmarks_fit %>%
plot_box_time() +
XXXXXX(axis.text.y = XXXXXX(),
axis.title.y = XXXXXX())## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
time_plot_clust <- benchmarks_clust %>%
plot_box_time() +
theme(legend.position = XXXXXX)## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
plot_XXXXXX(time_plot_clust, time_plot_fit, XXXXXX = "h", rel_widths = c(1,3))## Error in plot_XXXXXX(time_plot_clust, time_plot_fit, XXXXXX = "h", rel_widths = c(1, : could not find function "plot_XXXXXX"
Adapted from: https://wilkelab.org/cowplot/articles/plot_grid.html#joint-plot-titles
mph_per_kph <- 0.621371
rides <- read_csv('https://raw.githubusercontent.com/kelly-sovacool/strava/master/data/processed/activities.csv', col_types = cols()) %>%
filter(distance_mi > 1, as.character(type) == 'Ride') %>%
mutate(average_speed_mph = average_speed * mph_per_kph) %>%
select(distance_mi, average_speed_mph, moving_time_hrs, start_date)
# make a plot grid consisting of two panels
p1 <- ggplot(rides, aes(x = XXXXXX, y = distance_mi)) +
geom_XXXXXX(colour = "blue") +
theme_XXXXXX(12) +
XXXXXX_grid(minor = 'none')## Error in geom_XXXXXX(colour = "blue"): could not find function "geom_XXXXXX"
p2 <- ggplot(rides, aes(x = moving_time_hrs, y = XXXXXX)) +
geom_XXXXXX(colour = "green") +
theme_XXXXXX(12) +
background_XXXXXX(minor = 'none') +
theme(axis.title.y = element_XXXXXX())## Error in geom_XXXXXX(colour = "green"): could not find function "geom_XXXXXX"
plot_row <- plot_XXXXXX(p1, p2)## Error in plot_XXXXXX(p1, p2): could not find function "plot_XXXXXX"
# now add the title
title <- ggXXXX() +
draw_XXXXXX(
"Distance travelled with average speed and time spent moving",
fontface = 'bold',
x = 0,
hjust = 0
) +
XXXXXX(
# add margin on the left of the drawing canvas,
# so title is aligned with left edge of first plot
plot.margin = margin(0, 0, 0, 7)
)## Error in ggXXXX(): could not find function "ggXXXX"
plot_XXXXXX(XXXXXX, plot_row, ncol = XXXXXX,
# rel_heights values control vertical title margins
rel_heights = c(0.1, 1)
)## Error in plot_XXXXXX(XXXXXX, plot_row, ncol = XXXXXX, rel_heights = c(0.1, : could not find function "plot_XXXXXX"
Adapted from: https://wilkelab.org/cowplot/articles/drawing_with_on_plots.html#making-inset-plots
rides <- read_csv('https://raw.githubusercontent.com/kelly-sovacool/strava/master/data/processed/activities.csv', col_types = cols()) %>%
filter(distance_mi > 1, as.character(type) == 'Ride') %>%
select(distance_mi, start_date, year)
plot_point <- rides %>% ggplot(aes(start_date, XXXXXX)) +
XXXXXX(color='red') +
theme_minimal_grid(12)## Error in XXXXXX(color = "red"): could not find function "XXXXXX"
inset <- rides %>%
group_by(year) %>%
summarize(sum_distance_mi=sum(distance_mi)) %>%
ggplot(aes(XXXXXX, sum_distance_mi)) +
geom_bar(stat = "Identity", XXXXXX = "skyblue2", alpha = 0.7) +
labs(y='Total Distance (mi)') +
XXXXXX_XXXXXX_continuous(expand = expansion(mult = c(0, 0.05))) +
theme_XXXXXX_hgrid(11)## Warning: Ignoring unknown parameters: XXXXXX
## Error in XXXXXX_XXXXXX_continuous(expand = expansion(mult = c(0, 0.05))): could not find function "XXXXXX_XXXXXX_continuous"
ggdraw(plot_point + theme_XXXXXX_open(12)) +
draw_XXXXXX(inset, x = 0.1, y = .45, width = .5, height = .5) +
draw_XXXXXX_XXXXXX(
c("A", "B"),
c(0, 0.1),
c(1, 0.95),
size = 12
)## Error in ggdraw(plot_point + theme_XXXXXX_open(12)): object 'plot_point' not found
Adapted from: https://wilkelab.org/cowplot/articles/aligning_plots.html
# make up some non-sensical data
alpha_data <- tibble(sample = as.factor(1:10),
otu_count = runif(10, min = 0, max = 100),
alpha_div = rnorm(10, mean = 2, sd = 0.5)
)
plot_col <- alpha_data %>%
ggplot(aes(sample, otu_count)) +
XXXXXX_col(fill = "#6297E770") +
XXXXXX_XXXXXX_continuous(expand = expansion(mult = c(0, 0.05)),
position = "right") +
scale_x_discrete() +
XXXXXX_minimal_hgrid(11, rel_small = 1) +
XXXXXX(
panel.grid.major = element_XXXXXX(color = "#6297E770"),
axis.line.x = element_XXXXXX(),
axis.text.x = element_XXXXXX(),
axis.title.x = element_XXXXXX(),
axis.ticks = element_XXXXXX(),
axis.ticks.length = grid::unit(0, "pt"),
axis.text.y = element_XXXXXX(color = "#6297E7"),
axis.title.y = element_XXXXXX(color = "#6297E7")
)## Error in XXXXXX_col(fill = "#6297E770"): could not find function "XXXXXX_col"
plot_point <- alpha_data %>%
ggplot(aes(sample, alpha_div)) +
XXXXXX_XXXXXX(size = 3, color = "#D5442D") +
XXXXXX_XXXXXX_continuous(limits = c(0, 4.5)) +
theme_half_open(11, rel_small = 1) +
scale_XXXXXX_discrete() +
theme(
axis.ticks.y = element_XXXXXX(color = "#BB2D05"),
axis.text.y = element_XXXXXX(color = "#BB2D05"),
axis.title.y = element_XXXXXX(color = "#BB2D05"),
axis.line.y = element_XXXXXX(color = "#BB2D05")
)## Error in XXXXXX_XXXXXX(size = 3, color = "#D5442D"): could not find function "XXXXXX_XXXXXX"
aligned_plots <- XXXXXX_plots(plot_col, plot_point, align="hv", axis="tblr")## Error in XXXXXX_plots(plot_col, plot_point, align = "hv", axis = "tblr"): could not find function "XXXXXX_plots"
overlaid_plots <- XXXXXX(aligned_plots[[1]]) +
XXXXXX_plot(aligned_plots[[2]])## Error in XXXXXX(aligned_plots[[1]]): could not find function "XXXXXX"
overlaid_plots## Error in eval(expr, envir, enclos): object 'overlaid_plots' not found
Source: https://wilkelab.org/cowplot/articles/shared_legends.html
# plot 1
p1 <- ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
geom_XXXXXX() +
stat_smooth(method = "lm") +
facet_XXXXXX(. ~ Species) +
theme_half_open(12) +
background_grid(major = 'y', minor = "none") +
panel_border() +
XXXXXX(legend.position = "none")## Error in geom_XXXXXX(): could not find function "geom_XXXXXX"
# plot 2
p2 <- ggplot(iris, aes(Sepal.Length, fill = Species)) +
XXXXXX_density(alpha = .7) +
scale_XXXXXX_XXXXXX(expand = expansion(mult = c(0, 0.05))) +
theme_XXXXXX_open(12) +
XXXXXX(legend.justification = "top")## Error in XXXXXX_density(alpha = 0.7): could not find function "XXXXXX_density"
p2a <- p2 + XXXXXX(legend.position = "none")## Error in eval(expr, envir, enclos): object 'p2' not found
# plot 3
p3 <- ggplot(iris, aes(Sepal.Width, fill = Species)) +
geom_density(alpha = .7) +
XXXXXX_XXXXXX_continuous(expand = c(0, 0)) +
theme_half_XXXXXX(12) +
XXXXXX(legend.position = "none")## Error in XXXXXX_XXXXXX_continuous(expand = c(0, 0)): could not find function "XXXXXX_XXXXXX_continuous"
legend <- XXXXXX_XXXXXX(p2)## Error in XXXXXX_XXXXXX(p2): could not find function "XXXXXX_XXXXXX"
# align all plots vertically
plots <- XXXXXX_XXXXXX(p1, p2a, p3, align = 'v', axis = 'l')## Error in XXXXXX_XXXXXX(p1, p2a, p3, align = "v", axis = "l"): could not find function "XXXXXX_XXXXXX"
# put together the bottom row and then everything
bottom_row <- plot_XXXXXX(
plots[[2]], plots[[3]], legend,
labels = c("B", "C"),
rel_widths = c(1, 1, .3),
nrow = 1
)## Error in plot_XXXXXX(plots[[2]], plots[[3]], legend, labels = c("B", "C"), : could not find function "plot_XXXXXX"
plot_XXXXXX(plots[[1]], bottom_row, labels = c("A"), ncol = 1)## Error in plot_XXXXXX(plots[[1]], bottom_row, labels = c("A"), ncol = 1): could not find function "plot_XXXXXX"
A link to the source or inspiration is given under each code chunk. See the key branch for the exact solutions.
Many of these are taken directly from another source, in some cases with slight modifications. The original creators’ copyrights still apply; all are OSI-approved licenses.