绘制箱线图时，使用ggplot2使多面x轴文本成为R中的分组因子

Question

I am creating faceted box plots that are grouped by a variable. Instead of having the x-axis text be the factors for the x-axis variable I'd like the x-axis text to be the grouping variable.

However, I don't just want to use the grouping variable as my x-axis variable because I'd like the boxplots to cluster. Its hard to explain well. But I think its clear from the code and comments below.

Let me know if you have any suggestions or can help and thanks in advance!

    library(ggplot2) 
    library(scales)
    ln_clr <- "black"
    bk_clr <- "white"
    set.seed(1)

# Creates variables for a dataset
    donor = rep(paste0("Donor",1:3), each=40)
    machine = sample(rep(rep(paste0("Machine",1:4), each=1),30))
    gene = rep(paste0("Gene",LETTERS[1:5]), each=24)
    value = rnorm(24*5, mean=rep(c(0.5,10,1000,25000,8000), each=24), 
                  sd=rep(c(0.5,8,900,9000,3000), each=24))

# Makes all values positive
    for(m in 1:length(value)){
        if(value[m]<0){
            value[m] <- sqrt(value[m]*value[m])
        }
    }
# Creates a data frame from variables
    df = data.frame(donor, machine, gene, value)

# Adds a clone variable    
        clns <- LETTERS[1:4]
        k=1
        for(i in 1:nrow(df)/4){
            for(j in 1:length(clns)){
                df$clone[k] <- paste(df$donor[k],clns[j],sep="")
                    k = k+1
            }
        }
        df$clone <- as.factor(df$clone)


#*************************************************************************************************************************************
# Creates the facet of the machine but what I want on the x-axis is clone, not donor. 
# However, if I set x to clone it doesn't group the boxplots and its harder to read 
# the graph.
    bp1 <- ggplot(df, aes(x=donor, y=value, group=clone)) +
        stat_boxplot(geom ='errorbar', position = position_dodge(width = .83), 
                     width = 0.25, size = 0.7, coef = 1) +
        geom_boxplot(coef=1, outlier.shape = NA, position = position_dodge(width = .83), 
                     lwd = 0.3, alpha = 1, colour = ln_clr) +
        geom_point(position = position_dodge(width = 0.83), size = 1.8, alpha = 0.9, 
                    mapping=aes(group=clone)) +
        facet_wrap(~ machine, ncol=2, scales="free_x") 

    bp1 + scale_y_log10(expand = c(0, 0)) +
        theme(axis.text.x= element_text(size=rel(1), colour = "black", angle=45, hjust=1),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1))

# Creates the facet of the Donor and clusters the clones but doesn't facet the  
# machine. This could be okay if I could put spaces in between the different  
# machine values but not the donors and could remove the donor facet labels, and 
# only have the machine values show up once.
    bp2 <- ggplot(df, aes(x=clone, y=value)) +
        stat_boxplot(geom ='errorbar', position = position_dodge(width = .83),  
                     width = 0.25, size = 0.7, coef = 1) +
        geom_boxplot(coef=1, outlier.shape = NA, position = position_dodge(width = .83), 
                     lwd = 0.3, alpha = 1, colour = ln_clr) +
        geom_point(position = position_dodge(width = 0.83), size = 1.8, alpha = 0.9) +
        facet_wrap(machine ~ donor, scales="free_x", ncol=6) 

    bp2 + scale_y_log10(expand = c(0, 0)) +
        theme(axis.text.x= element_text(size=rel(1), colour = "black", angle=45, hjust=1),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1),
              panel.spacing = unit(0, "lines"))    

Below is an example comparing what I'd like in an ideal world (Top two facets) as compared to what I'm getting (bottom two facets).

Answer 1

I'm not sure I understand exactly what you're trying to do, so let me know if this is on the right track:

library(dplyr)

pd = position_dodge(width=0.83)

ggplot(df %>% mutate(clone=gsub("Donor[1-3]","",clone),
                     donor=gsub("Donor", "", donor)), 
       aes(x=clone, y=value, color=donor, group=interaction(clone,donor))) +
  geom_boxplot(coef=1, outlier.shape=NA, position=pd, lwd=0.3) +
  geom_point(position=pd, size=1.8, alpha=0.9) +
  facet_wrap(~ machine, ncol=2, scales="free_x") +
  scale_y_log10(expand = c(0.02, 0)) +
  theme(strip.background=element_rect(colour=ln_clr, fill=bk_clr, size=1)) 

How about this:

ggplot(df, aes(x=clone, y=value, group=interaction(clone,donor))) +
  geom_boxplot(coef=1, outlier.shape=NA, lwd=0.3) +
  geom_point(size=1.8, alpha=0.9) +
  facet_wrap(~ machine, ncol=2, scales="free_x") +
  scale_y_log10(expand = c(0.02, 0)) +
  theme(axis.text.x= element_text(size=rel(1), colour = "black", angle=45, hjust=1),
        strip.background=element_rect(colour=ln_clr, fill=bk_clr, size=1)) 

Answer 2

I found a work around for this problem but its not very elegant. I'd be super happy if some one came up with a better solution. Using the code to create a function for a "multiplot" found here and adding the code below I was able to do what I wanted. However, This is a slightly wonky solution in that I can't really format my titles with boxes around them and there are still two "clone" titles on the x axis that I can't replace easily with a single x-axis title. Also, had I of had many "machines" in my example this solution would have been painful to scale. All-in-all not ideal but passible for what I need. Special thanks to Eipi10 for their help, I appreciate it.

# Creates a multi-plot function for use in the graphs below   
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))
        }
    }
}

    # Call multiplot function after storing each of the below plots as variables
    ln_clr <- "black"
    bk_clr <- "white"

    bp3 <- ggplot(df[df$machine=="Machine1",], aes(x=clone, y=value)) +
        geom_boxplot(coef=1, outlier.shape=NA, lwd=0.3) +
        geom_point(size=1.8, alpha=0.9) +
        ggtitle("Machine 1") + 
        expand_limits(y=c(0.001,10^5)) +
        facet_wrap(~ donor, nrow=1, scales="free_x") + scale_y_log10(expand = c(0, 0)) +
        theme(axis.text.x= element_text(size=rel(1), color = ln_clr, angle=45, hjust=1),
              panel.spacing = unit(0.25, "lines"), axis.title.x= element_blank(),
              plot.title = element_text(hjust=0.5), 
              strip.text.x = element_text(size=rel(1), face="bold", colour = ln_clr),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1),
              axis.line.x= element_line(size = 1.25, colour = ln_clr),
              axis.line.y= element_line(size = 1.25, colour = ln_clr),
              panel.grid.major = element_blank(), 
              panel.grid.minor = element_blank(), 
              panel.background = element_rect(fill = bk_clr),
              panel.border = element_blank(),
              plot.background = element_rect(fill = bk_clr))

    bp4 <- ggplot(df[df$machine=="Machine2",], aes(x=clone, y=value)) +
        geom_boxplot(coef=1, outlier.shape=NA, lwd=0.3) +
        geom_point(size=1.8, alpha=0.9) +
        ggtitle("Machine 2") + 
        expand_limits(y=c(0.001,10^5)) +
        facet_wrap(~ donor, nrow=1, scales="free_x") + scale_y_log10(expand = c(0, 0)) +
        theme(axis.text.x= element_text(size=rel(1), colour = ln_clr, angle=45, hjust=1),
              panel.spacing = unit(0.25, "lines"), plot.title = element_text(hjust=0.5),
              strip.text.x = element_text(size=rel(1), face="bold", colour = ln_clr),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1),
              axis.line.x= element_line(size = 1.25, colour = ln_clr),
              axis.line.y= element_line(size = 1.25, colour = ln_clr),
              panel.grid.major = element_blank(), 
              panel.grid.minor = element_blank(), 
              panel.background = element_rect(fill = bk_clr),
              panel.border = element_blank(),
              plot.background = element_rect(fill = bk_clr))

    bp5 <- ggplot(df[df$machine=="Machine3",], aes(x=clone, y=value)) +
        geom_boxplot(coef=1, outlier.shape=NA, lwd=0.3) +
        geom_point(size=1.8, alpha=0.9) +
        ggtitle("Machine 3") + 
        expand_limits(y=c(0.001,10^5)) +
        facet_wrap(~ donor, nrow=1, scales="free_x") + scale_y_log10(expand = c(0, 0)) +
        theme(panel.spacing = unit(0.25, "lines"), axis.title.y= element_blank(),
              axis.title.x= element_blank(),axis.line.y= element_blank(),
              axis.text.y=element_blank(),
              axis.text.x= element_text(size=rel(1), colour = ln_clr, angle=45, hjust=1),
              axis.ticks.y=element_blank(), plot.title = element_text(hjust=0.5),
              strip.text.x = element_text(size=rel(1), face="bold", colour = ln_clr),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1),
              axis.line.x= element_line(size = 1.25, colour = ln_clr),
              panel.grid.major = element_blank(), 
              panel.grid.minor = element_blank(), 
              panel.background = element_rect(fill = bk_clr),
              panel.border = element_blank(),
              plot.background = element_rect(fill = bk_clr))

    bp6 <- ggplot(df[df$machine=="Machine4",], aes(x=clone, y=value)) +
        geom_boxplot(coef=1, outlier.shape=NA, lwd=0.3) +
        geom_point(size=1.8, alpha=0.9) +
        ggtitle("Machine 4") + 
        expand_limits(y=c(0.001,10^5)) +
        facet_wrap(~ donor, nrow=1, scales="free_x") + scale_y_log10(expand = c(0, 0)) +
        theme(axis.text.x= element_text(size=rel(1), colour = ln_clr, angle=45, hjust=1),
              panel.spacing = unit(0.25, "lines"), plot.title = element_text(hjust=0.5),
              strip.text.x = element_text(size=rel(1), face="bold", colour = ln_clr),
              strip.background = element_rect(colour = ln_clr, fill = bk_clr, size = 1),
              axis.line.x= element_line(size = 1.25, colour = ln_clr),
              axis.line.y= element_blank(),
              axis.text.y=element_blank(),
              axis.ticks.y=element_blank(),
              axis.title.y= element_blank(),
              panel.grid.major = element_blank(), 
              panel.grid.minor = element_blank(), 
              panel.background = element_rect(fill = bk_clr),
              panel.border = element_blank(),
              plot.background = element_rect(fill = bk_clr))

# Plot all 4 graphs and saves them as a output file  
    png(filename="graph3.png", width= 9, height= 7.5, units = "in", res=600)
    multiplot(bp3, bp4, bp5, bp6, cols=2)
    dev.off()

Alternatively, if I set the "strip.text.x = " and the "strip.background =" as element_blank(). I can generate the below: