介绍

有时候我们需要将多个图像排列好放到一张图上，对于R语言基础包的函数，比如plot， barplot， hist等，是可以通过par, layout进行排版，但是对于ggplot的图像，我们需要使用别的方法

几种方法实现

传统的par和layout的方法

par方法

方法只适用于基础包的函数(plot, barplot, hist等)，不适用于ggplot。

par(mfrow = c(1,2))
plot(mtcars[,1:2],pch =19)
plot(iris[,1:2],pch = 19)

layout方法

layout(matrix(c(2,0,1,3),2,2,byrow=TRUE), widths=c(3,1), heights=c(1,3), respect=TRUE)

设置布局，布局矩阵是

2  0 
1  3

表示左下是第一个画，左上是第二个，右下是第三个画，右上不画图。widths = c(3,1)表示从左到右宽度比是3比1，heights=c(1,3)表示高度从上到下是1比三, respect=True单位列宽与单位行高在设备上是相同的物理度量

示例如下

#读入数据
air<-read.csv("airpollution.csv")

#首先设置布局
layout(matrix(c(2,0,1,3),2,2,byrow=TRUE), widths=c(3,1), heights=c(1,3), TRUE)

#画散点图
par(mar=c(5.1,4.1,0.1,0))
plot(air$Respirable.Particles~air$Nitrogen.Oxides,pch=19,
col="black",xlim=c(0,600),ylim=c(0,80),xlab="Nitrogen Oxides Concentrations",ylab="Respirable Particle Concentrations")

#画X的直方图，在散点图的上方
par(mar=c(0,4.1,3,0))
hist(air$Nitrogen.Oxides,breaks=seq(0,600,100),ann=FALSE,axes=FALSE,
col="black",border="white")

#画Y的直方图，在散点图的右方
yhist <- hist(air$Respirable.Particles,breaks=seq(0,80,10),plot=FALSE)
par(mar=c(5.1,0,0.1,1))
barplot(yhist$density,horiz=TRUE,space=0,axes=FALSE,col="black",border="white")

ggplot的可以使用ggpubr包的函数ggarange

使用install.packages("ggpubr")安装ggpubr包。

ggarrange(..., 
    plotlist = NULL, 
    ncol = NULL, 
    nrow = NULL, 
    labels = NULL,
    label.x = 0, 
    label.y = 1, 
    hjust = -0.5, 
    vjust = 1.5,
    font.label = list(size = 14, color = "black", face = "bold", family = NULL),
    align = c("none", "h", "v", "hv"), 
    widths = 1, 
    heights = 1,
    legend = NULL,
    common.legend = FALSE)

  …：需要画的图对象,可以直接放放多个ggplot的对象
  plotlist，也可以将ggplot对象放到列表里，给到这个plotlist参数
  ncol和nrow是要排列成几行几列
  labels每个图的标签，label.x label.y hjust vjust font.label都是调整labels的位置参数，
  align各个图的排列方式，是纵向(v)还是横向排列(h)，
  widths和heights调整各图的长宽比列
  legend是各图的图例，
  commn.legend公共的图例

示例如下

cols <- brewer.pal(n=5, name=\'Set1\')  #配置色板
# 用plist存放ggplot对象，再用ggarrange进行排版并画图
plist <- list()
plist[[1]] <- ggplot(df1,aes(x=sample,y=count,fill=group))+theme_classic()+geom_bar(stat=\'identity\')+
  theme(legend.position = "none", 
        axis.title.x=element_blank(),
        axis.text.x=element_blank(),
        axis.ticks.x=element_blank()) + 
  ylab(\'HMR#\')+
  scale_fill_manual(values=c(\'darkgray\',cols))
plist[[2]] <- ggplot(df3,aes(x=sample,y=count,fill=group))+theme_classic()+geom_bar(stat=\'identity\')+
  theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank(),legend.position = "none")+
  scale_fill_brewer(palette=\'Dark2\')+ylab(\'CpG#\')
plist[[3]] <- ggplot(df5,aes(x=sample,y=percent.copy.altered,fill=namecn))+theme_classic()+geom_bar(stat=\'identity\')+
  theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank(),legend.position = "none")+
  scale_fill_manual(values=\'darkgrey\')+ylab(\'% CN Altered\')
plist[[4]] <- ggplot(df5,aes(x=sample,y=mutation_count,fill=namemut))+theme_classic()+geom_bar(stat=\'identity\')+
  theme(axis.title.x=element_blank(),axis.text.x=element_blank(),axis.ticks.x=element_blank(),legend.position = "none")+
  scale_fill_manual(values=\'darkgrey\')+ylab(\'Mut/Mb\')+scale_y_log10() 

plist[[5]] <- ggplot(df6,aes(x=sample,y=count,fill=group))+theme_classic()+geom_bar(stat=\'identity\')+
  theme(axis.title.x=element_blank(),
        axis.text.x=element_text(angle=90,hjust=1,vjust=0.5,colour=df6$color),
        axis.ticks.x=element_blank(),
        legend.position = "none")+ 
  scale_fill_brewer(palette=\'Set2\')+ylab(\'# SV\')

ggarrange(plotlist=plist,
          ncol=1,
          nrow=length(plist),
          heights=c(3,1,1,1,2) ,
          align="v")
ggsave(fn_fig1a, height=8, width=14)

ggplot的也可以使用grid排版

grid包是R语言自带的底层的绘图系统，可以比较细的对图，线条，点等进行排版布局。我们这里包装成一个函数，用法跟ggarrange很像。
示例：

# Multiple plot function
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot
# objects)
# - cols:   Number of columns in layout
# - layout: A matrix specifying the layout. If present, \'cols\' is ignored.
#
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
# e=0.15, # extra height needed for last plot (vertical layout),
# or extra width for first plot (horizontal layout)
multiplot <- function(..., plotlist=NULL, file, cols=1,
                      layout=NULL, horizontal=FALSE, e=0.15) {
  require(grid)

  # Make a list from the ... arguments and plotlist
  plots = c(list(...), plotlist)

  numPlots = length(plots)
  #message(paste0(\'>>>>>>>INFO: num plots 2 = \', numPlots), \'\n\')

  # If layout is NULL, then use \'cols\' to determine layout
  if (is.null(layout)) {
    # Make the panel
    # ncol: Number of columns of plots
    # nrow: Number of rows needed, calculated from # of cols
    layout = matrix(seq(1, cols * ceiling(numPlots/cols)),
                    ncol = cols, nrow = ceiling(numPlots/cols))
  }

  if (numPlots==1) {
    print(plots[[1]])

  } else {

    ## set up heights/widths of plots

    # extra height needed for last plot (vertical layout),
    # or extra width for first plot (horizontal layout)
    hei = rep(1, numPlots)
    # bottom plot is taller
    hei[numPlots] = hei[numPlots]*(1+e)
    wid = rep(1, numPlots)
    # first left plot is wider
    wid[1] = wid[1]*(1+e)
    # Set up the page
    grid.newpage()
    if(horizontal){
      pushViewport(viewport(layout = grid.layout(nrow(layout),
                                                 ncol(layout), widths=wid)))
    }else{
      pushViewport(viewport(layout = grid.layout(nrow(layout),
                                                 ncol(layout), heights=hei)))

    }

    # Make each plot, in the correct location
    for (i in 1:numPlots) {
      # Get i,j matrix positions of the regions containing this subplot
      matchidx = as.data.frame(which(layout == i, arr.ind = TRUE))
      print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
                                      layout.pos.col = matchidx$col))
    }
  }
}

library(ggplot2)
p1 <- ggplot(iris, aes(x = Sepal.Length)) + geom_histogram() + theme_bw()
p2 <- ggplot(iris, aes(x = Sepal.Length, y = Petal.Width)) + geom_point() + theme_bw()

# 直接使用ggplot对象画图
multiplot(p1,p2)

# 将ggplot对象放入列表中，再用列表画图, 并设置两列的排列方式
plot_lst <- list()
plot_lst[[1]] <- p1
plot_lst[[2]] <- p2
multiplot(plotlist = plot_lst, cols = 2)