Plotting with ggplot2
ggplot2 is a powerful framework for
visualization. In this section, we’ll assume some basic familiarity with
the package; if you’re new to ggplot2, this primer may be
helpful.
tidyfun provides
tf_ggplot() as the primary interface for plotting
functional data with ggplot2. It works
just like ggplot(), but understands tf vectors
— use the tf aesthetic to map a tf column to
the plot, then add standard ggplot2 geoms
(geom_line, geom_point,
geom_ribbon, etc.).
For heatmaps, use gglasagna; for
sparklines / glyphs on maps, use
geom_capellini (these use their own
specialized stats and are called directly without
tf_ggplot). The older geoms
geom_spaghetti,
geom_meatballs, and
geom_errorband remain available for
backward compatibility.
tf_ggplot with standard geoms
One of the most fundamental plots for functional data is the
spaghetti plot, which is implemented in
tidyfun and
ggplot2 through tf_ggplot() +
geom_line():
Adding geom_point() to geom_line() shows
both the curves and the observed data values:
Using with other ggplot2 features
tf_ggplot() plays nicely with standard
ggplot2 aesthetics and options.
You can, for example, define the color aesthetic for plots of
tf variables using other observations:
chf_df |>
filter(id %in% 1:5) |>
tf_ggplot(
aes(tf = tf_smooth(activity, f = .05), # smoothed inputs for clearer viz
color = gender)) +
geom_line(alpha = 0.3)
… or use facetting:
chf_df |>
filter((id %in% 1:10) & (day %in% c("Mon", "Sun"))) |>
tf_ggplot(aes(tf = tf_smooth(activity, f = .05), color = gender)) +
geom_line(alpha = 0.3, lwd = 1) +
facet_grid(~day)
Another example, using the DTI data, is below.
dti_df |>
tf_ggplot(aes(tf = cca, col = case, alpha = 0.2 + 0.4 * (case == "control"))) +
geom_line() + facet_wrap(~sex) +
scale_alpha(guide = "none", range = c(0.2, 0.4))
Together with tidyfun’s tools for
functional data wrangling and summary statistics, the integration with
ggplot2 can produce useful exploratory
analyses, like the plot below showing group-wise smoothed and unsmoothed
mean activity profiles:
chf_df |>
group_by(gender, day) |>
summarize(mean_act = mean(activity),
.groups = "drop_last") |>
mutate(smooth_mean = tfb(mean_act, verbose = FALSE)) |>
filter(day %in% c("Mon", "Sun")) |>
tf_ggplot(aes(color = gender)) +
geom_line(aes(tf = smooth_mean), linewidth = 1.25) +
geom_line(aes(tf = mean_act), alpha = 0.1) +
geom_point(aes(tf = mean_act), alpha = 0.1, size = .1) +
facet_grid(day~.)
… or the plot below showing group-wise mean functions +/- twice their pointwise standard errors:
dti_df |>
group_by(sex, case) |>
summarize(
mean_cca = mean(tfb(cca, verbose = FALSE)), #pointwise mean function
sd_cca = sd(tfb(cca, verbose = FALSE)), # pointwise sd function
.groups = "drop_last"
) |>
group_by(sex, case) |>
mutate(
upper_cca = mean_cca + 2 * sd_cca,
lower_cca = mean_cca - 2 * sd_cca
) |>
tf_ggplot() +
geom_line(aes(tf = mean_cca, color = sex)) +
geom_ribbon(aes(tf_ymin = lower_cca, tf_ymax = upper_cca, fill = sex), alpha = 0.3) +
facet_grid(sex ~ case)
Functional data boxplots with geom_fboxplot
“Boxplots” for functional data are implemented in
tidyfun through geom_fboxplot(). They show the
deepest function (using modified band depth, "MBD", by
default) as a thick median curve, a filled central ribbon spanning the
pointwise range of the deepest half of the sample (by default), and
outer fence lines obtained by inflating that central envelope by a
factor of coef = 1.5. Curves that leave the fence envelope
anywhere are flagged as outliers and drawn separately.
Like geom_boxplot(), the layer follows the usual
ggplot2 interface closely. Grouping works
naturally through colour, fill, or
group, and the same group colour is reused for the ribbon,
the outlier curves, and the median if a group colour/fill is mapped;
otherwise, the median defaults to black.
dti_df |>
tf_ggplot(aes(tf = cca, fill = case)) +
geom_fboxplot(alpha = 0.35) +
facet_grid(~ sex) + labs(title="MBD-based boxplot")
dti_df |>
tf_ggplot(aes(tf = cca, colour = case)) +
geom_fboxplot(depth = "FM", alpha = 0.3) +
facet_grid(~ sex) + labs(title="FM-based boxplot")
dti_df |>
tf_ggplot(aes(tf = cca, colour = case)) +
geom_fboxplot(depth = "RPD", alpha = 0.3) +
facet_grid(~ sex) + labs(title="RPD-based boxplot")
The layer also supports irregular functional data directly:
Useful arguments:
Heatmaps for functional data: gglasagna
Lasagna plots are “a saucy alternative
to spaghetti plots”. They are a variant on a heatmaps which show
functional observations in rows and use color to illustrate values taken
at different arguments. Especially for large samples or noisy data,
lasagna plots can be more informative than spaghetti plots, which can be
hard to read when many curves are plotted together. Lasagna plots also
allow for easy visual comparison of groups of curves, and the
order argument in gglasagna() allows you to
sort the curves by any variable or function of the data, which can help
reveal patterns in the data.
In tidyfun, lasagna plots are
implemented through gglasagna (as well as a basic
plot method, see ?!?). A first example, using the CHF data,
is below.
A somewhat more involved example, demonstrating the
order argument and taking advantage of facets, is next.
dti_df |>
gglasagna(
tf = cca,
order = tf_integrate(cca, definite = TRUE), #order by area under the curve
arg = seq(0, 1, length.out = 101)
) +
theme(axis.text.y = element_text(size = 6)) +
facet_wrap(~ case:sex, ncol = 2, scales = "free")
geom_capellini
To illustrate geom_capellini, we’ll start with some data
prep for the iconic Canadian Weather data from
fda:
canada <- data.frame(
place = fda::CanadianWeather$place,
region = fda::CanadianWeather$region,
lat = fda::CanadianWeather$coordinates[, 1],
lon = -fda::CanadianWeather$coordinates[, 2]
)
canada$temp <- tfd(t(fda::CanadianWeather$dailyAv[, , 1]), arg = 1:365)
canada$precipl10 <- tfd(t(fda::CanadianWeather$dailyAv[, , 3]), arg = 1:365) |>
tf_smooth()
## Using `f = 0.15` as smoother span for `lowess()`.
canada_map <-
data.frame(maps::map("world", "Canada", plot = FALSE)[c("x", "y")])Now we can plot a map of Canada with annual temperature averages in red, precipitation in blue:
ggplot(canada, aes(x = lon, y = lat)) +
geom_capellini(aes(tf = precipl10),
width = 4, height = 5, colour = "blue",
line.linetype = 1
) +
geom_capellini(aes(tf = temp),
width = 4, height = 5, colour = "red",
line.linetype = 1
) +
geom_path(data = canada_map, aes(x = x, y = y), alpha = 0.1) +
coord_quickmap()
Another general use case for geom_capellini is
visualizing FPCA decompositions:
cca_fpc_tbl <- tibble(
cca = dti_df$cca[1:30],
cca_fpc = tfb_fpc(cca, pve = .8),
fpc_1 = map(coef(cca_fpc), 2) |> unlist(), # 1st PC loading
fpc_2 = map(coef(cca_fpc), 3) |> unlist() # 2nd PC loading
)
# rescale FPCs by sqrt of eigenvalues for visualization
cca_fpcs_1_2 <-
tf_basis(cca_fpc_tbl$cca_fpc, as_tfd = TRUE)[2:3] *
sqrt(attr(cca_fpc_tbl$cca_fpc, "score_variance")[1:2])
# scaled eigenfunctions look like this:
tibble(
eigenfunction = cca_fpcs_1_2,
FPC = factor(1:2)
) |> tf_ggplot() +
geom_line(aes(tf = eigenfunction, col = FPC)) +
geom_hline(yintercept = 0)
So FPC1 is mostly a horizontal (level) shift, while FPC2 mostly affects the size and direction of the extrema around 0.13 and 0.8.
ggplot(cca_fpc_tbl[1:40,], aes(x = fpc_1, y = fpc_2)) +
geom_point(size = .5, col = viridis(3)[2]) +
geom_capellini(aes(tf =cca_fpc),width = .01, height = .01, line.linetype = 1) +
labs(x = "FPC1 score", y = "FPC2 score")
Consequently, we can see here that the horizontal axis representing the
1st FPC scores has the average level of functions increasing from left
to right (first FPC function is basically a level shift), while the size
and direction of the extrema at around 0.13 and particularly 0.8 change
along the vertical axis representing the 2nd FPC scores.
