使用ggviolin函数绘制小提琴图
加载所需R包
library(ggpubr)
基本用法：
ggviolin(data, x, y, combine = FALSE, merge = FALSE, color = "black",
fill = "white", palette = NULL, title = NULL, xlab = NULL,
ylab = NULL, facet.by = NULL, panel.labs = NULL,
short.panel.labs = TRUE, linetype = "solid", trim = FALSE,
size = NULL, width = 1, draw_quantiles = NULL, select = NULL,
remove = NULL, order = NULL, add = "mean_se", add.params = list(),
error.plot = "pointrange", label = NULL, font.label = list(size = 11,color = "black"),
label.select = NULL, repel = FALSE,
label.rectangle = FALSE, ggtheme = theme_pubr(), ...)
常用参数：
Arguments
data #a data frame
x #character string containing the name of x variable.
y #character vector containing one or more variables to plot
combine #logical value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, create a multi-panel plot by combining the plot of y variables.
merge #logical or character value. Default is FALSE. Used only when y is a vector containing multiple variables to plot. If TRUE, merge multiple y variables in the same plotting area. Allowed values include also "asis" (TRUE) and "flip". If merge = "flip", then y variables are used as x tick labels and the x variable is used as grouping variable.
color #outline color.
fill #fill color.
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".
title #plot main title.
xlab #character vector specifying x axis labels. Use xlab = FALSE to hide xlab.
ylab #character vector specifying y axis labels. Use ylab = FALSE to hide ylab.
facet.by #character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.
panel.labs #a list of one or two character vectors to modify facet panel labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies the labels for the "sex" variable. For two grouping variables, you can use for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs", "Lev", "Lev2") ).
short.panel.labs #logical value. Default is TRUE. If TRUE, create short labels for panels by omitting variable names; in other words panels will be labelled only by variable grouping levels.
linetype #line types.
trim #是否去除离群点 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 #是否添加分位数线 If not(NULL) (default), draw horizontal lines at the given quantiles of the density estimate.
select #character vector specifying which items to display.
remove #character vector specifying which items to remove from the plot.
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, ....
label #the name of the column containing point labels. Can be also a character vector with length = nrow(data).
font.label #a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").
repel #a logical value, whether to use ggrepel to avoid overplotting text labels or not.
label.rectangle #logical value. If TRUE, add rectangle underneath the text, making it easier to read.
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, ggpar and facet.
使用示例：
Examples
# Load data
data("ToothGrowth")
df <- ToothGrowth
head(df)
## len supp dose
## 1 4.2 VC 0.5
## 2 11.5 VC 0.5
## 3 7.3 VC 0.5
## 4 5.8 VC 0.5
## 5 6.4 VC 0.5
## 6 10.0 VC 0.5
# Basic plot
p1 <- ggviolin(df, x = "dose", y = "len")
p1
p1
# Change the plot orientation: horizontal
p2 <- ggviolin(df, "dose", "len", orientation = "horiz")
p2
p2
# Add summary statistics
# Draw quantiles 添加分位数线
p3 <- ggviolin(df, "dose", "len", add = "none",
draw_quantiles = 0.5)
p3
p3
# Add box plot 添加箱线图和点图
p4 <- ggviolin(df, x = "dose", y = "len",
add = "boxplot")
p4
p4
p5 <- ggviolin(df, x = "dose", y = "len",
add = "dotplot")
p5
p5
# Add jitter points and 添加扰动点
# change point shape by groups ("dose")
p6 <- ggviolin(df, x = "dose", y = "len",
add = "jitter", shape = "dose")
p6
p6
# Add mean_sd + jittered points
p7 <- ggviolin(df, x = "dose", y = "len",
add = c("jitter", "mean_sd"))
p7
p7
# Change error.plot to "crossbar"
p8 <- ggviolin(df, x = "dose", y = "len",
add = "mean_sd", error.plot = "crossbar")
p8
p8
# Change colors
# Change outline and fill colors
p9 <- ggviolin(df, "dose", "len",
color = "black", fill = "gray")
p9
p9
# Change outline colors by groups: dose
# Use custom color palette and add boxplot
p10 <- ggviolin(df, "dose", "len", color = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
add = "boxplot")
p10
p10
# Change fill color by groups: dose
# add boxplot with white fill color
p11 <- ggviolin(df, "dose", "len", fill = "dose",
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
add = "boxplot", add.params = list(fill = "white"))
p11
p11
# Plot with multiple groups
# fill or color box plot by a second group : "supp"
p12 <- ggviolin(df, "dose", "len", color = "supp",
palette = c("#00AFBB", "#E7B800"), add = "boxplot")
p12
p12
p13 <- ggviolin(df, "dose", "len", facet.by = "supp", color = "supp",
palette = c("#00AFBB", "#E7B800"), add = "boxplot")
p13
p13
参考来源：
https://www.rdocumentation.org/packages/ggpubr/versions/0.1.4/topics/ggviolin
sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggpubr_0.1.7.999 magrittr_1.5 ggplot2_3.0.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.18 rstudioapi_0.7 bindr_0.1.1 knitr_1.20
## [5] tidyselect_0.2.4 munsell_0.5.0 colorspace_1.3-2 R6_2.2.2
## [9] rlang_0.2.2 stringr_1.3.1 plyr_1.8.4 dplyr_0.7.6
## [13] tools_3.5.1 grid_3.5.1 gtable_0.2.0 withr_2.1.2
## [17] htmltools_0.3.6 assertthat_0.2.0 yaml_2.2.0 lazyeval_0.2.1
## [21] rprojroot_1.3-2 digest_0.6.16 tibble_1.4.2 crayon_1.3.4
## [25] bindrcpp_0.2.2 purrr_0.2.5 glue_1.3.0 evaluate_0.11
## [29] rmarkdown_1.10 labeling_0.3 stringi_1.2.4 compiler_3.5.1
## [33] pillar_1.3.0 scales_1.0.0 backports_1.1.2 pkgconfig_2.0.2
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