ggpubr (version 0.1.1)

ggviolin: Violin plot

Description

Create a violin plot with error bars. Violin plots are similar to box plots, except that they also show the kernel probability density of the data at different values.

Usage

ggviolin(data, x, y, color = "black", fill = "white", palette = NULL, linetype = "solid", trim = FALSE, size = NULL, width = 1, draw_quantiles = NULL, select = NULL, order = NULL, add = "mean_se", add.params = list(), error.plot = "pointrange", ggtheme = theme_classic2(), ...)

Arguments

data

a data frame

x, y

x and y variables for drawing.

color, fill

outline and fill colors.

palette

the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".

linetype

line types.

trim

If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails.

size

Numeric value (e.g.: size = 1). change the size of points and outlines.

width

violin width.

draw_quantiles

If not(NULL) (default), draw horizontal lines at the given quantiles of the density estimate.

select

character vector specifying which items to display.

order

character vector specifying the order of items.

add

character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_mad", "median_range"; see ?desc_statby for more details.

add.params

parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").

error.plot

plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....

ggtheme

function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

...

other arguments to be passed to geom_violin.

Details

The plot can be easily customized using the function ggpar(). Read ?ggpar for changing:

• main title and axis labels: main, xlab, ylab
• axis limits: xlim, ylim (e.g.: ylim = c(0, 30))
• axis scales: xscale, yscale (e.g.: yscale = "log2")
• color palettes: palette = "Dark2" or palette = c("gray", "blue", "red")
• legend title, labels and position: legend = "right"
• plot orientation : orientation = c("vertical", "horizontal", "reverse")

See Also

ggpar

Examples

# Load data
data("ToothGrowth")
df <- ToothGrowth

# Basic plot
# +++++++++++++++++++++++++++
ggviolin(df, x = "dose", y = "len")
# Change the plot orientation: horizontal
ggviolin(df, "dose", "len", orientation = "horiz")

# Add summary statistics
# ++++++++++++++++++++++++++
# Draw quantiles
ggviolin(df, "dose", "len", add = "none",
   draw_quantiles = 0.5)

# Add box plot
ggviolin(df, x = "dose", y = "len",
 add = "boxplot")

ggviolin(df, x = "dose", y = "len",
 add = "dotplot")

# Add jitter points and
# change point shape by groups ("dose")
ggviolin(df, x = "dose", y = "len",
add = "jitter", shape = "dose")


# Add mean_sd + jittered points
ggviolin(df, x = "dose", y = "len",
 add = c("jitter", "mean_sd"))

# Change error.plot to "crossbar"
ggviolin(df, x = "dose", y = "len",
 add = "mean_sd", error.plot = "crossbar")


# Change colors
# +++++++++++++++++++++++++++
# Change outline and fill colors
ggviolin(df, "dose", "len",
   color = "black", fill = "gray")

# Change outline colors by groups: dose
# Use custom color palette and add boxplot
ggviolin(df, "dose", "len",  color = "dose",
   palette = c("#00AFBB", "#E7B800", "#FC4E07"),
   add = "boxplot")

# Change fill color by groups: dose
# add boxplot with white fill color
ggviolin(df, "dose", "len", fill = "dose",
   palette = c("#00AFBB", "#E7B800", "#FC4E07"),
   add = "boxplot", add.params = list(fill = "white"))


# Plot with multiple groups
# +++++++++++++++++++++
# fill or color box plot by a second group : "supp"
ggviolin(df, "dose", "len", color = "supp",
 palette = c("#00AFBB", "#E7B800"), add = "boxplot")