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Last data update: 2014.03.03

R: Create a violin plot

plot_ViolinPlot

R Documentation

Create a violin plot

Description

Draws a kernal densiy plot in combination with a boxplot in its middle. The shape of the violin is constructed using a mirrored density curve. This plot is especially designed for cases where the individual errors are zero or to small to be visualised. The idea for this plot is based on the the 'volcano plot' in the ggplot2 package by Hadely Wickham and Winston Chang. The general idea for the Violin Plot seems to be introduced by Hintze and Nelson (1998).

Usage

plot_ViolinPlot(data, boxplot = TRUE, rug = TRUE, summary = NULL,
  summary.pos = "sub", na.rm = TRUE, ...)

Arguments

`data`	`numeric` or `RLum.Results` object (required): input data for plotting. Alternatively a `data.frame` or a `matrix` can be provided, but only the first column will be considered by the function
`boxplot`	`logical` (with default): enable or disable boxplot
`rug`	`logical` (with default): enable or disable rug
`summary`	`character` (optional): add statistic measures of centrality and dispersion to the plot. Can be one or more of several keywords. See details for available keywords.
`summary.pos`	`numeric` or `character` (with default): optional position keywords (cf., `legend`) for the statistical summary. Alternatively, the keyword `"sub"` may be specified to place the summary below the plot header. However, this latter option in only possible if `mtext` is not used.
`na.rm`	`logical` (with default): exclude NA values from the data set prior to any further operations.
`...`	further arguments and graphical parameters passed to `plot.default`, `density` and `boxplot`. See details for further information

Details

The function is passing several arguments to the function plot, density, boxplot: Supported arguments are: xlim, main, xlab, ylab, col.violin, col.boxplot, mtext, cex, mtext

Valid summary keywords

'n', 'mean', 'median', 'sd.abs', 'sd.rel', 'se.abs', 'se.rel', 'skewness', 'kurtosis'

Function version

0.1.2 (2016-05-17 13:27:04)

Note

Although the code for this function was developed independently and just the idea for the plot was based on the 'ggplot2' package plot type 'volcano', it should be mentioned that, beyond this, two other R packages exist providing a possibility to produces this kind of plot, namely: 'vioplot' and 'violinmplot' (see References for details).

Author(s)

Sebastian Kreutzer, IRAMAT-CRP2A, Universite Bordeaux Montaigne (France)
R Luminescence Package Team

References

Daniel Adler (2005). vioplot: A violin plot is a combination of a box plot and a kernel density plot. R package version 0.2 http://CRAN.R-project.org/package=violplot

Hintze, J.L., Nelson, R.D., 1998. A Box Plot-Density Trace Synergism. The American Statistician 52, 181-184.

Raphael W. Majeed (2012). violinmplot: Combination of violin plot with mean and standard deviation. R package version 0.2.1. http://CRAN.R-project.org/package=violinmplot

Wickham. H (2009). ggplot2: elegant graphics for data analysis. Springer New York.

Examples

## read example data set
data(ExampleData.DeValues, envir = environment())
ExampleData.DeValues <- Second2Gray(ExampleData.DeValues$BT998, c(0.0438,0.0019))

## create plot straightforward
plot_ViolinPlot(data = ExampleData.DeValues)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Luminescence)
Welcome to the R package Luminescence version 0.6.0 [Built: 2016-05-30 16:47:30 UTC]
A fluvially transported quartz grain at night: 'Always look at the bright side of life.'
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Luminescence/plot_ViolinPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_ViolinPlot
> ### Title: Create a violin plot
> ### Aliases: plot_ViolinPlot
> 
> ### ** Examples
> 
> ## read example data set
> data(ExampleData.DeValues, envir = environment())
> ExampleData.DeValues <- Second2Gray(ExampleData.DeValues$BT998, c(0.0438,0.0019))
> 
> ## create plot straightforward
> plot_ViolinPlot(data = ExampleData.DeValues)
Warning message:
[plot_ViolinPlot()] 2 NA values removed! 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>