ggpubr包学习笔记之轻松修改图形参数

2017-09-13 本文已影响279人 taoyan

简介

越学习包ggpubr越感觉其功能强大，本文主要讲解一下如何修改图形参数，我们知道ggplot2有着十分强大的绘图功能，但是其参数之复杂足以让人望而却步。ggpubr提供的函数ggpar()可以十分轻松地让我们修改图形参数，并且可以无缝对接到ggplot图形中。ggpar()可以修改以下图形参数：

图形标题，包括坐标轴标题以及图例标题
图例的位置以及外观
颜色必需的能修改
坐标轴limits
坐标转换
坐标刻度
主题
翻转等

安装包

#two ways to isntall the ggpubr package
install.packages("ggpubr")
#install the packages from the Github
devtools::install_github("kassambara/ggpubr")

绘图

library(ggpubr)#load ggpubr
#basic plots
p <- ggboxplot(ToothGrowth, x="dose", y="len", color="dose")
p

#add grids by the function grids()
p+grids(linetype="dashed")

#add panel borders lines by the function border()
p+border("black")

#change background color
p+bgcolor("#BFD5E3")+border("#BFD5E3")

修改标题以及坐标轴标签

p2 <- ggpar(p,
            title = "Box plot created with ggpubr",
            subtitle = "Length by dose",
            caption = "Source: ggpubr",
            xlab = "Dose (mg)",
            ylab = "Teeth length",
            legend.title = "Dose (mg)")
p2

修改标题以及标签的字体

ggpar(p2, 
      font.title = c(14, "bold.italic", "red"),
      font.subtitle = c(10, "orange"),
      font.caption = c(10, "orange"),
      font.x = c(14, "blue"),
      font.y = c(14, "#993333"))

当然也可以直接用函数font()

p2+
  font("title", size = 14, color = "red", face = "bold.italic")+
  font("subtitle", size = 10, color = "orange")+
  font("caption", size = 10, color = "orange")+
  font("xlab", size = 12, color = "blue")+
  font("ylab", size = 12, color = "#993333")

从上面可以看出我们可以一次性完成添加标题以及修改字体

ggpar(p,
      title = "Plot of length \n by dose",
      xlab = "Dose (mg)",
      legend.title = "Dose (mg)",
      font.title = c(14, "bold.italic", "red"),
      font.x = c(14, "bold", "#2E9FDF"),
      font.y = c(14, "bold", "#E7B800"))

修改图例位置与外观

ggpar(p,
      legend = "right", legend.title = "Dose (mg)")+
  font("legend.title", color="blue", face = "bold")+
  font("legend.text", color = "red")

颜色修改

ggpar()中有一个参数palette，即调色板，除了可以我们自定义颜色外，还可以调用RColorBrewer中的调色板以及包ggsci中的专门用于学术杂志的配色。

#use custom color palette
ggpar(p, palette = c("#00AFBB", "#E7B800", "#FC4E07"))

#use the RColorBrewer palette
ggpar(p, palette = "Dark2")

ggpar(p, palette = "grey")

#use the ggsci palette
ggpar(p, palette = "npg")#nature

当然也可以直接用ggpubr中的函数color_palette()以及fill_palette()

#jco color palette
p+color_palette("jco")

#custom color
p+color_palette(c("#00AFBB", "#E7B800", "#FC4E07"))

颜色梯度

ggpubr提供了两个函数用来处理颜色梯度：gradient_color()和gradient_fill()
通过一个例子来看如何运作

#first create a scatter plot
p3 <- ggscatter(mtcars, x="wt", y="mpg", color="mpg", size = 2)
#change the gradient color
#use one custom color
p3+gradient_color("red")

#use two colors
p3+gradient_color(c("blue", "red"))

#three colors
p3+gradient_color(c("blue", "white", "red"))

#use the RColorBrewer palette
p3+gradient_color("RdYlBu")

gradient_fill()用法也一样，不过是填充，这里就不演示了。

修改坐标轴limits、scales

#change y axis limits
ggpar(p, ylim = c(0, 50))

#change y axis cale to log2
ggpar(p, yscale = "log2")

#format  axis scale
ggpar(p, yscale = "log2", format.scale = TRUE)#format.scale=TRUE说明y轴刻度也会scale

#也可以直接用yscale()
p+yscale("log2", .format = TRUE)

自定义坐标轴标签及刻度

#change the font of x and y axis texts
#rotate x and y texts
p+
  font("xy.text", size = 12, color = "blue", face = "bold")+
  rotate_x_text(45)+
  rotate_y_text(45)

#remove ticks and axis texts
p+rremove("ticks")+
  rremove("axis.text")

修改主题

默认主题为theme_pubr(),可以调用包ggthemes里面的主题

library(ggthemes)
p+ggthemes::theme_economist()

移除ggplot组件

通过ggpubr::rremove()可以移除组件：

p <- ggboxplot(ToothGrowth, x="dose", y="len", ggtheme = theme_igray())
p

p+rremove("grid")

SessionInfo

sessionInfo()

## R version 3.4.1 (2017-06-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
## 
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
## 
## locale:
##  [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
##  [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
##  [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggthemes_3.4.0 ggpubr_0.1.5   magrittr_1.5   ggplot2_2.2.1 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.12       bindr_0.1          knitr_1.17        
##  [4] munsell_0.4.3      colorspace_1.3-2   R6_2.2.2          
##  [7] rlang_0.1.2        stringr_1.2.0      plyr_1.8.4        
## [10] dplyr_0.7.3        tools_3.4.1        grid_3.4.1        
## [13] gtable_0.2.0       htmltools_0.3.6    yaml_2.1.14       
## [16] lazyeval_0.2.0     rprojroot_1.2      digest_0.6.12     
## [19] assertthat_0.2.0   tibble_1.3.4       bindrcpp_0.2      
## [22] ggsci_2.7          RColorBrewer_1.1-2 purrr_0.2.3       
## [25] glue_1.1.1         evaluate_0.10.1    rmarkdown_1.6     
## [28] labeling_0.3       stringi_1.1.5      compiler_3.4.1    
## [31] scales_0.5.0       backports_1.1.0    pkgconfig_2.0.1

联系方式：

wechat: yt056410
Email: tyan@zju.edu.cn
QQ: 1051927088
GitHub: https://github.com/YTLogos
简书: http://www.jianshu.com/u/bd001545cf0b
博客: https://ytlogos.github.io/

个人简介：

严涛
浙江大学作物遗传育种在读研究生（生物信息学方向）
伪码农，R语言爱好者，爱开源