pdf将图表保存在彼此之上而不是网格中

Question

我正在尝试在pdf中输出两个 ggplot 图表列表。我想制作一个pdf文件，其中左边有一个列表，右边有一个列表（理想情况下是4个2格的多页）。

我包含所有代码只是为了彻底，但重要的部分是绘图。

如果我在R studio中运行它，我会在图表预览中看到我想要的内容，但如果我包含在 pdf（文件名）和 dev.off <之间打印图表的循环/ em>我得到一个单页的pdf文件，其中所有的图都在彼此之上。我到处都看，但我无法让它发挥作用。

library(ggplot2)
library(tools)
library(gridExtra)
library(grid)

data_ahl<-read.csv("data_AHL.txt", header = TRUE)
data_none<-read.csv("data_none.txt", header = TRUE)

data_ahl$Concentration <- as.factor(data_ahl$Concentration)
data_none$Concentration <- as.factor(data_none$Concentration)

data <- rbind(data_ahl, data_none)

plasmid_list <- unique(data_ahl$Plasmid)
plot_list_atc <- list()
plot_list_none <- list()
j = 1

for (receiver in plasmid_list){
  print(receiver)
  upperbound <- max(data_ahl$GFP)
  a <- subset(data_ahl, Plasmid == receiver)
  plot_atc <- ggplot(a, aes(x = GFP)) + 
    geom_density(color = 'green') +
    ggtitle(label = c(receiver, "induced with aTC")) +
    xlab("GFP") +
    ylab("Density") +
    theme_minimal() +
    scale_x_continuous(limits = c(0,upperbound))

  b <- subset(data_none, Plasmid == receiver)
  plot_none <- ggplot(b, aes(x = GFP)) + 
    geom_density(color = 'green') +
    labs(title = c(receiver, "no induction")) +
    xlab("GFP") +
    ylab("Density") +
    theme_minimal() +
    scale_x_continuous(limits = c(0,upperbound))


  plot_list_atc[[j]] <- plot_atc
  plot_list_none[[j]] <- plot_none
  j = j+1

}

#----PLOTTING-----
grid.newpage()
main.vp <- viewport(layout = grid.layout(11,2))
pushViewport(main.vp)

pdf("receiver_plots.pdf", paper = "a4")

nplots <- length(plot_list_atc) 

row = 1
for (i in 1:nplots){
  print(plot_list_none[[i]], vp = viewport(layout.pos.row = row,
                                           layout.pos.col = 1))
  print(plot_list_atc[[i]], vp = viewport(layout.pos.row = row,
                                          layout.pos.col = 2))
  row = row + 1

}
dev.off()

Answer 1

您必须先打开pdf设备，然后布局网格：

#----PLOTTING-----
pdf("receiver_plots.pdf", paper = "a4")

grid.newpage()
main.vp <- viewport(layout = grid.layout(11,2))
pushViewport(main.vp)

nplots <- length(plot_list_atc) 

row = 1
for (i in 1:nplots){
  print(plot_list_none[[i]], vp = viewport(layout.pos.row = row,
                                           layout.pos.col = 1))
  print(plot_list_atc[[i]], vp = viewport(layout.pos.row = row,
                                          layout.pos.col = 2))
  row = row + 1

}
dev.off()

Answer 2

也许您可以尝试multiplot功能我正在使用。

# 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.
#
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
  library(grid)

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

  numPlots = length(plots)

  # 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 the page
    grid.newpage()
    pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))

    # Make each plot, in the correct location
    for (i in 1:numPlots) {
      # Get the i,j matrix positions of the regions that contain 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))
    }
  }
}

p1到p5是我的ggplot对象，在一列中对齐

multiplot(p1,p2,p3,p4,p5,cols=1)

Answer 3

感谢大家的回答，我最终设法解决了我的问题。显然，在声明视口之前必须打开pdf设备。我还设法以4乘2格的形式制作了这些地块。

我包含代码以防有人发现它有用。

#----PLOTTING-----
pdf("receiver_plots.pdf", width = 10, height = 15)
grid.newpage()
main.vp <- viewport(layout = grid.layout(4,2))
pushViewport(main.vp)

nplots <- length(plot_list_atc) 
row = 1

for (i in 1:nplots){

  print(plot_list_none[[i]], vp = viewport(layout.pos.row = row,
                                           layout.pos.col = 1))
  print(plot_list_atc[[i]], vp = viewport(layout.pos.row = row,
                                          layout.pos.col = 2))
  if (row == 4){

    grid.newpage()
    main.vp <- viewport(layout = grid.layout(4,2))
    pushViewport(main.vp)
    row = 1
  } else {
    row = row + 1
  }
}

dev.off()