The post How to create a ggalluvial plot in R? appeared first on Data Science Tutorials

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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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