Easily generate violin plots using ggplot2 with a simplified customization interface for common modifications with static (ggplot) and interactive (plotly) output options. The static output is useful for producing static reports (e.g. for manuscripts) and is readily customized further using ggplot2 syntax. The interactive output is helpful for exploring the data and producing dynamic html reports. See this blog post for an introduction to ggplot2.

plot_violin(
  data,
  y,
  x = NULL,
  ...,
  fill_var = NULL,
  colour_var = NULL,
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  title_hjust = 0.5,
  caption = NULL,
  caption_hjust = 0,
  fill_var_title = NULL,
  colour_var_title = NULL,
  ylim = c(NA, NA),
  ybreaks = ggplot2::waiver(),
  transform_y = FALSE,
  y_transformation = "log10",
  y_var_labs = ggplot2::waiver(),
  x_var_order = NULL,
  x_var_labs = NULL,
  fill_var_order = NULL,
  colour_var_order = NULL,
  fill_var_labs = NULL,
  colour_var_labs = NULL,
  fill_var_values = NULL,
  colour_var_values = NULL,
  palette = c("plasma", "C", "magma", "A", "inferno", "B", "viridis", "D", "cividis",
    "E"),
  palette_direction = c("d2l", "l2d"),
  palette_begin = 0,
  palette_end = 1,
  alpha = 0.75,
  greyscale = FALSE,
  line_size = 1,
  theme = c("bw", "classic", "grey", "light", "dark", "minimal"),
  text_size = 14,
  font = c("sans", "serif", "mono"),
  facet_var = NULL,
  facet_var_order = NULL,
  facet_var_labs = NULL,
  facet_var_strip_position = c("top", "bottom"),
  facet_var_text_bold = TRUE,
  legend_position = c("right", "left", "top", "bottom"),
  omit_legend = FALSE,
  interactive = FALSE,
  aesthetic_options = FALSE
)

Arguments

data

A data frame or tibble containing the dependent measure "y" and any grouping variables.

y

A numeric variable you want to obtain violin plots for (quoted or unquoted), e.g. y = "variable" or y = variable.

x

A categorical variable you want to obtain separate violin plots of y for (quoted or unquoted), e.g. x = "variable" or x = variable.

...

graphical parameters (not associated with variables) to be passed to geom_violin, e.g. colour or fill, to be applied to all bars. To see some of the available options in a web browser, set the aesthetic_options argument to TRUE. An option unique to geom_violin is draw_quantiles, which adds horizontal lines for the specified quantiles, e.g. draw_quantiles = c(0.25, 0.5, 0.75) would add lines for the 25th, 50th, and 75th percentiles (similar to a boxplot).

fill_var

Use if you want to assign a variable to the violin fill colour, e.g. fill_var = "grouping_variable" or fill_var = grouping_variable. Produces separate sets of bars for each level of the fill variable. See aes for details.

colour_var

Use if you want to assign a variable to the violin outline colour, e.g. colour_var = "grouping_variable" or colour_var = grouping_variable. Produces separate sets of bars for each level of the colour variable. See aes for details.

xlab

Specify/overwrite the x-axis label using a character string, e.g. "x-axis label"

ylab

Specify/overwrite the y-axis label using a character string, e.g. "y-axis label"

title

Add a main title to the plot using a character string, e.g. "Violin graph of X"

title_hjust

Left-to-right/horizontal justification (alignment) of the main plot title. Accepts values from 0 (far left) to 1 (far right). Default is 0.5 (centre).

caption

Add a figure caption to the bottom of the plot using a character string.

caption_hjust

Left-to-right/horizontal justification (alignment) of the caption. Accepts values from 0 (far left) to 1 (far right). Default is 0 (left).

fill_var_title

If a variable has been assigned to fill using fill_var, this allows you to modify the variable label in the plot legend.

colour_var_title

If a variable has been assigned to colour using colour_var, this allows you to modify the variable label in the plot legend.

ylim

specify the y-axis limits, e.g. ylim = c(lower_limit, upper_limit). Use NA for the existing minimum or maximum value of y, e.g. the default is ylim = c(NA, NA)

ybreaks

This allows you to change the break points to use for tick marks on the y-axis. seq is particularly useful here. See scale_y_continuous for details. If ybreaks is specified, then ylim should be also.

transform_y

Would you like to transform the y axis? (TRUE or FALSE)

y_transformation

If transform_y = TRUE, this determines the transformation to be applied. Common choices include "log10" (the default), "log2", "sqrt", or "exp". See scale_continuous for details.

y_var_labs

Allows you to modify the labels displayed with the y-axis tick marks. See scale_continuous for details.

x_var_order

If a variable has been assigned to x, this allows you to modify the order of the variable groups, e.g. x = grouping_variable, x_var_order = c("group_2", "group_1"). See fct_relevel for details.

x_var_labs

If a variable has been assigned to x, this allows you to modify the labels of the variable groups, e.g. x = grouping_variable, x_var_labs = c("group_1_new_label" = "group_1_old_label", "group_2_new_label" = "group_2_old_label"). See fct_recode for details.

fill_var_order

If a variable has been assigned to fill using fill_var, this allows you to modify the order of the variable groups, e.g. fill_var = grouping_variable, fill_var_order = c("group_2", "group_1"). See fct_relevel for details.

colour_var_order

If a variable has been assigned to colour using colour_var, this allows you to modify the order of the variable groups, e.g. colour_var = grouping_variable, fill_var_order = c("group_2", "group_1"). See fct_relevel for details.

fill_var_labs

If a variable has been assigned to fill using fill_var, this allows you to modify the labels of the variable groups, e.g. fill_var = grouping_variable, fill_var_labs = c("group_1_new_label" = "group_1_old_label", "group_2_new_label" = "group_2_old_label"). See fct_recode for details.

colour_var_labs

If a variable has been assigned to colour using colour_var, this allows you to modify the labels of the variable groups, e.g. colour_var = grouping_variable, colour_var_labs = c("group_1_new_label" = "group_1_old_label", "group_2_new_label" = "group_2_old_label"). See fct_recode for details.

fill_var_values

If a variable has been assigned to fill using fill_var, this allows you to modify the colours assigned to the fill of each of the variable groups, e.g. fill_var = grouping_variable, fill_var_values = c("blue", "red"). See scale_fill_manual for details. For the colour options available in base R, see colour_options.

colour_var_values

If a variable has been assigned to colour using colour_var, this allows you to modify the colours assigned to the outline of each of the variable groups, e.g. colour_var = grouping_variable, colour_var_values = c("blue", "red"). See scale_fill_manual for details. For the colour options available in base R, see colour_options.

palette

If a variable is assigned to fill_var or colour_var, this determines which viridis colour palette to use. Options include "plasma" or "C" (default), "magma" or "A", "inferno" or "B", "viridis" or "D", and "cividis" or "E". See this link for examples. You can override these colour palettes with fill_var_values or colour_var_values.

palette_direction

Choose "d2l" for dark to light (default) or "l2d" for light to dark.

palette_begin

Value between 0 and 1 that determines where along the full range of the chosen colour palette's spectrum to begin sampling colours. See scale_fill_viridis_d for details.

palette_end

Value between 0 and 1 that determines where along the full range of the chosen colour palette's spectrum to end sampling colours. See scale_fill_viridis_d for details.

alpha

This adjusts the transparency/opacity of the graphical components of the plot, ranging from 0 = 100% transparent to 1 = 100% opaque.

greyscale

Set to TRUE if you want the plot converted to greyscale.

line_size

Controls the thickness of the violin outlines.

theme

Adjusts the theme using 1 of 6 predefined "complete" theme templates provided by ggplot2. Currently supported options are: "classic", "bw" (the elucidate default), "grey" (the ggplot2 default), "light", "dark", & "minimal". See theme_bw for more information.

text_size

This controls the size of all plot text. Default = 14.

font

This controls the font of all plot text. Default = "sans" (Arial). Other options include "serif" (Times New Roman) and "mono" (Courier New).

facet_var

Use if you want separate plots for each level of a grouping variable (i.e. a faceted plot), e.g. facet_var = "grouping_variable" or facet_var = grouping_variable. See facet_wrap for details.

facet_var_order

If a variable has been assigned for faceting using facet_var, this allows you to modify the order of the variable groups, e.g. facet_var = grouping_variable, facet_var_order = c("group_2", "group_1"). See fct_relevel for details.

facet_var_labs

If a variable has been assigned for faceting using facet_var, this allows you to modify the labels of the variable groups which will appear in the facet strips, e.g. facet_var = grouping_variable, facet_var_labs = c("group_1_new_label" = "group_1_old_label", "group_2_new_label" = "group_2_old_label"). See fct_recode for details.

facet_var_strip_position

If a variable has been assigned for faceting using facet_var, this allows you to modify the position of the facet strip labels. Sensible options include "top" (the default) or "bottom".

facet_var_text_bold

If a variable has been assigned for faceting using facet_var, this allows you to use boldface (TRUE/default or FALSE) for the facet strip label text.

legend_position

This allows you to modify the legend position. Options include "right" (the default), "left", "top", & "bottom".

omit_legend

Set to TRUE if you want to remove/omit the legends.

interactive

Determines whether a static ggplot object or an interactive html plotly object is returned. See ggplotly for details.

aesthetic_options

If set to TRUE, opens a web browser to the tidyverse online aesthetic options vignette.

Value

A ggplot object or plotly object depending on whether static or interactive output was requested.

References

Wickham, H. (2016). ggplot2: elegant graphics for data analysis. New York, N.Y.: Springer-Verlag.

See also

Author

Craig P. Hutton, craig.hutton@gov.bc.ca

Examples

data(mtcars) #load the mtcars data

plot_violin(mtcars, y = mpg, x = cyl, fill = "blue")


plot_violin(mtcars, y = mpg, x = cyl,
            fill = "blue", draw_quantiles = c(0.25, 0.5, 0.75))


# \donttest{
plot_violin(mtcars, x = cyl, y = hp,
           xlab = "# of cylinders",
           ylab = "horsepower",
           fill_var = am,
           fill_var_title = "transmission",
           fill_var_labs = c("manual" = "0", "automatic" = "1"),
           fill_var_values = c("blue", "red"),
           theme = "bw")


#modifying fill doesn't work as well for the interactive version of a boxplot
plot_violin(mtcars, x = cyl, y = hp,
           xlab = "# of cylinders",
           ylab = "horsepower",
           fill_var = am,
           fill_var_title = "transmission",
           fill_var_labs = c("manual" = "0", "automatic" = "1"),
           fill_var_values = c("blue", "red"),
           theme = "bw",
           interactive = TRUE)
#using colour works better for the interactive version plot_violin(mtcars, x = cyl, y = hp, xlab = "# of cylinders", ylab = "horsepower", colour_var = am, colour_var_title = "transmission", colour_var_labs = c("manual" = "0", "automatic" = "1"), colour_var_values = c("blue", "red"), theme = "bw", interactive = TRUE)
# }