How to create a ggalluvial plot in R, The ggalluvial package’s vaccines data set includes a survey “that asked respondents their likelihood of receiving an influenza vaccination.”
The discretized probability of immunization, the frequency of respondents, and the survey’s designation make up the response variable.
Let’s install ggalluvial package
install.packages("ggalluvial")
library(ggalluvial)
head(vaccinations)survey freq subject response start_date end_date 1 ms153_NSA 48 1 Always 2010-09-22 2010-10-25 2 ms153_NSA 9 2 Always 2010-09-22 2010-10-25 3 ms153_NSA 66 3 Always 2010-09-22 2010-10-25 4 ms153_NSA 1 4 Always 2010-09-22 2010-10-25 5 ms153_NSA 11 5 Always 2010-09-22 2010-10-25 6 ms153_NSA 1 6 Always 2010-09-22 2010-10-25
Alluvial plot
To construct alluvial diagrams in ggplot2, use the geom alluvium and geom stratum functions from the ggalluvial package.
You must utilize the aforementioned routines, pass your data in long format, and specify the axis variables inside the aes.
You can also alter the ggplot2 theme, add the text for each stratum, and add the names of the axis variables, albeit you won’t see them in the examples that follow because we set theme_void.
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
More categorical variables in your dataset can be passed to aes (axis1, axis2, axis3,…) as in the example below.
ggplot(data = vaccinations,
aes(axis1 = survey, # First variable on the X-axis
axis2 = response, # Second variable on the X-axis
axis3 = survey, # Third variable on the X-axis
y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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With the curve type input of the geom alluvium function, the type of flows in the plot region can be modified.
The “xspline” value by default creates approximation splines with four points per curve. The alternate options are as follows:
Linear
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "linear") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Cubic
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "cubic") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Quintic
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "quintic") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Sine
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "sine") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Arctangent
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "arctangent") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Sigmoid
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response),
curve_type = "sigmoid") +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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For alternative curve types based on asymptotic functions, take note that there is an additional argument entitled curve range. Enter geom alluvium for more information.
Customization of colours
The colours used for the flows can be changed. They can have a single colour assigned to them, a predetermined colour palette, or a custom colour vector.
Note that the stratum boxes’ colours can also be changed.
Fill color
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = "red")) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
scale_fill_viridis_d()
theme_void()
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Color palette
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
scale_fill_viridis_d() +
theme_void()
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Custom colors
colors <- hcl.colors(4, "Red-Blue")
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
scale_fill_manual(values = colors) +
theme_void()
Stratum color
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum(aes(fill = response)) +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void()
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Legend customization
Since the ggalluvial program was developed using ggplot2, it is possible to alter the legend of the plots’ titles, key labels, and positions, or even delete them entirely, as demonstrated in the examples below.
The legend of the alluvial diagram should be renamed.
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void() +
guides(fill = guide_legend(title = "Title"))
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Legend key labels
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void() +
scale_fill_hue(labels = c("A", "B", "C", "D"))
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Remove the legend
ggplot(data = vaccinations,
aes(axis1 = survey, axis2 = response, y = freq)) +
geom_alluvium(aes(fill = response)) +
geom_stratum() +
geom_text(stat = "stratum",
aes(label = after_stat(stratum))) +
scale_x_discrete(limits = c("Survey", "Response"),
expand = c(0.15, 0.05)) +
theme_void() +
theme(legend.position = "none")
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