ggpubr包系列学习教程(十三)
2018-09-11 本文已影响5人
Davey1220
使用ggerrorplot函数绘制误差棒图
加载所需R包
library(ggpubr)
基本用法：
Usage
ggerrorplot(data, x, y, desc_stat = "mean_se", combine = FALSE,
merge = FALSE, color = "black", fill = "white", palette = NULL,
size = NULL, width = NULL, title = NULL, xlab = NULL, ylab = NULL,
facet.by = NULL, panel.labs = NULL, short.panel.labs = TRUE,
select = NULL, remove = NULL, order = NULL, add = "none",
add.params = list(), error.plot = "pointrange",
position = position_dodge(), ggtheme = theme_pubr(), ...)
常用参数：
Arguments
data #a data frame
x, y #x and y variables for drawing.
desc_stat #选择展示误差的统计量 descriptive statistics to be used for visualizing errors. Default value is "mean_se". Allowed values are one of , "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_mad", "median_range"; see desc_statby for more details.
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, 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".
size #Numeric value (e.g.: size = 1). change the size of points and outlines.
width #numeric value between 0 and 1 specifying box width.
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.
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, ....
position #Position adjustment, either as a string, or the result of a call to a position adjustment function.
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 be passed to ggpar().
使用示例：
Examples
# Data: ToothGrowth data set we'll be used.
df<- ToothGrowth
head(df, 10)
## 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
## 7 11.2 VC 0.5
## 8 11.2 VC 0.5
## 9 5.2 VC 0.5
## 10 7.0 VC 0.5
# Plot mean_se
p1 <- ggerrorplot(df, x = "dose", y = "len")
p1
p1
# Change desc_stat to mean_sd
# (other values include: mean_sd, mean_ci, median_iqr, ....)
# Add labels
p2 <- ggerrorplot(df, x = "dose", y = "len",
desc_stat = "mean_sd")
p2
p2
# Change error.plot to "errorbar" and add mean point
# Visualize the mean of each group
p3 <- ggerrorplot(df, x = "dose", y = "len",
add = "mean", error.plot = "errorbar")
p3
p3
# Horizontal plot
p4 <- ggerrorplot(df, x = "dose", y = "len",
add = "mean", error.plot = "errorbar",
orientation = "horizontal")
p4
p4
# Change error.plot to "crossbar"
p5 <- ggerrorplot(df, x = "dose", y = "len",
error.plot = "crossbar", width = 0.5)
p5
p5
# Add jitter points and errors (mean_se)
p6 <- ggerrorplot(df, x = "dose", y = "len", color="dose",
add = "jitter")
p6
p6
# Add dot and errors (mean_se)
p7 <- ggerrorplot(df, x = "dose", y = "len",
add = "dotplot")
p7
p7
# Multiple groups with error bars and jitter point
p8 <- ggerrorplot(df, x = "dose", y = "len",
color = "dose", palette = "Paired",
error.plot = "pointrange",
position = position_dodge(0.5))
p8
p8
参考来源：
https://www.rdocumentation.org/packages/ggpubr/versions/0.1.4/topics/ggerrorplot
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
## [4] knitr_1.20 tidyselect_0.2.4 munsell_0.5.0
## [7] colorspace_1.3-2 R6_2.2.2 rlang_0.2.2
## [10] 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
## [16] withr_2.1.2 htmltools_0.3.6 assertthat_0.2.0
## [19] yaml_2.2.0 lazyeval_0.2.1 rprojroot_1.3-2
## [22] digest_0.6.16 tibble_1.4.2 crayon_1.3.4
## [25] bindrcpp_0.2.2 RColorBrewer_1.1-2 purrr_0.2.5
## [28] glue_1.3.0 evaluate_0.11 rmarkdown_1.10
## [31] labeling_0.3 stringi_1.2.4 compiler_3.5.1
## [34] pillar_1.3.0 scales_1.0.0 backports_1.1.2
## [37] pkgconfig_2.0.2
