完美契合ggplot2绘图的情节

Question

我想绘制一个受限制的三次样条曲线作为主图,并添加一个盒子和须状图来显示X变量的变化.然而,下铰链(x = 42),中间(x = 51)和上铰链(x = 61)与主曲线的相应网格线不完全吻合.

library(Hmisc)
library(rms)
library(ggplot2)
library(gridExtra)

data(pbc)
d <- pbc
rm(pbc)
d$status <- ifelse(d$status != 0, 1, 0)

dd = datadist(d)
options(datadist='dd')

f <- cph(Surv(time, status) ~  rcs(age, 4), data=d)
p <- Predict(f, fun=exp)
df <- data.frame(age=p$age, yhat=p$yhat, lower=p$lower, upper=p$upper)

### 1st PLOT: main plot
(g <- ggplot(data=df, aes(x=age, y=yhat)) + geom_line(size=1))

# CI
(g <- g + geom_ribbon(data=df, aes(ymin=lower, ymax=upper), alpha=0.5, linetype=0, fill='#FFC000'))

# white background
(g <- g + theme_bw())

# X-axis
(breaks <- round(boxplot.stats(p[,"age"])$stats))
(g <- g + scale_x_continuous(breaks=breaks, limits=range(p[,"age"]), labels=round(breaks)))
(g <- g + xlab("Age"))

# Y-Achse
(g <- g + ylab("Hazard Ratio"))

# size and color of axis
(g <- g + theme(axis.line = element_line(color='black', size=1)))
(g <- g + theme(axis.ticks = element_line(color='black', size=1)))

(g <- g + theme( plot.background = element_blank() ))
#(g <- g + theme( panel.grid.major = element_blank() ))
(g <- g + theme( panel.grid.minor = element_blank() ))
(g <- g + theme( panel.border = element_blank() ))

### 2nd PLOT: box whisker plot
describe(df$age, digits=0)
round(range(df$age))
(gg <- ggplot(data=df, aes(x=1, y=age)) + geom_boxplot(outlier.shape=NA, size=1) + coord_flip())
(gg <- gg + theme( axis.line=element_blank() )) #
(gg <- gg + theme( axis.text.x=element_blank() ))
(gg <- gg + theme( axis.text.y=element_blank() ))
(gg <- gg + theme( axis.ticks=element_blank() ))
(gg <- gg + theme( axis.title.x=element_blank() ))
(gg <- gg + theme( axis.title.y=element_blank() ))
(gg <- gg + theme( panel.background=element_blank() ))
(gg <- gg + theme( panel.border=element_blank() )) #
(gg <- gg + theme( legend.position="none" )) #
(gg <- gg + theme( panel.grid.major=element_blank() )) #
(gg <- gg + theme( panel.grid.minor=element_blank() ))
(gg <- gg + theme( plot.background=element_blank() ))
(gg <- gg + theme( plot.margin = unit( c(0,0,0,0), "in" ) ))

(gg <- gg + scale_x_continuous(breaks=c(70,77,84), expand=c(0,0)) )

### FINAL PLOT: put box whisker plot in main plot
(final.gg <- g + annotation_custom(ggplotGrob(gg),  ymin=2.4, ymax=2.6))

1. 为了完美契合,我需要改变什么？
2. 盒式和须式的y位置的自动对齐是否更好？

更新#1 感谢您的回答!下面你可以看到我的代码示例.但是,如您所见,下铰链,中间和上铰链仍然不适合.出了什么问题？

library(Hmisc)
library(rms)
library(ggplot2)
library(gridExtra)

data(pbc)
d <- pbc
rm(pbc, pbcseq)
d$status <- ifelse(d$status != 0, 1, 0)

dd = datadist(d)
options(datadist='dd')

f <- cph(Surv(time, status) ~  rcs(age, 4), data=d)
p <- Predict(f, fun=exp)
df <- data.frame(age=p$age, yhat=p$yhat, lower=p$lower, upper=p$upper)

### 1st PLOT: main plot
(breaks <- boxplot.stats(p[,"age"])$stats)
g <- ggplot(data=df, aes(x=age, y=yhat)) + geom_line(size=1) +
     geom_ribbon(data=df, aes(ymin=lower, ymax=upper), alpha=0.5, linetype=0, fill='#FFC000') +
     theme_bw() +
     scale_x_continuous(breaks=breaks) +
     xlab("Age") +
     ylab("Hazard Ratio") +
     theme(axis.line = element_line(color='black', size=1),
           axis.ticks = element_line(color='black', size=1),
           plot.background = element_blank(),
           # panel.border = element_blank(),
           panel.grid.minor = element_blank())

### 2nd PLOT: box whisker plot
gg <- ggplot(data=df, aes(x=1, y=age)) + 
     geom_boxplot(outlier.shape=NA, size=1) + 
     scale_y_continuous(breaks=breaks) +
     ylab(NULL) +
     coord_flip()  + 
     # theme_bw() +
     theme(axis.line=element_blank(), 
           # axis.text.x=element_blank(),
           axis.text.y=element_blank(),
           axis.ticks.y=element_blank(), 
           axis.title=element_blank(),
           # panel.background=element_blank(),
           panel.border=element_blank(),
           # panel.grid.major=element_blank(),
           panel.grid.minor=element_blank(),
           # plot.background=element_blank(),
           plot.margin = unit( c(0,0,0,0), "in" ), 
           axis.ticks.margin = unit(0, "lines"),
           axis.ticks.length = unit(0, "cm"))

### FINAL PLOT: put box whisker plot in main plot
(final.gg <- g + annotation_custom(ggplotGrob(gg),  ymin=2.4, ymax=2.6))

Answer 1

小编辑：更新到 ggplot2 2.0.0 axis.ticks.margin已弃用

在箱线图中，即使您已将各种元素element_blank和边距设置为零，默认空格仍然会导致未对齐。这些空间属于：

• 轴.刻度.长度
• 实验室

在下面的代码中，我稍微重新安排了您的代码（我希望没关系），并注释掉了一些代码行，以便可以看到这两个图确实对齐。我还将两个图中的中断设置为不四舍五入breaks（最小值和最大值、铰链和中值）。

# X-axis
(breaks <- boxplot.stats(p[,"age"])$stats)

### 1st PLOT: main plot
g <- ggplot(data=df, aes(x=age, y=yhat)) + geom_line(size=1) +
     geom_ribbon(data=df, aes(ymin=lower, ymax=upper), alpha=0.5, linetype=0, fill='#FFC000') +
     theme_bw() +
     scale_x_continuous(breaks=breaks) +
     xlab("Age") +
     ylab("Hazard Ratio") +
     theme(axis.line = element_line(color='black', size=1),
       axis.ticks = element_line(color='black', size=1),
       plot.background = element_blank(),
      # panel.border = element_blank(),
       panel.grid.minor = element_blank())

### 2nd PLOT: box whisker plot
gg <- ggplot(data=df, aes(x=1, y=age)) + 
      geom_boxplot(outlier.shape=NA, size=1) + 
      scale_y_continuous(breaks=breaks) +
      xlab(NULL) +
      coord_flip()  + 
     # theme_bw() +
      theme(axis.line=element_blank(), 
         # axis.text.x=element_blank(),
          axis.text.y=element_blank(),
          axis.ticks.y=element_blank(), 
          axis.title=element_blank(),
         # panel.background=element_blank(),
          panel.border=element_blank(),
         # panel.grid.major=element_blank(),
          panel.grid.minor=element_blank(),
         # plot.background=element_blank(),
          plot.margin = unit( c(0,0,0,0), "in" ), 
         # axis.ticks.margin = unit(0, "lines"),
          axis.ticks.length = unit(0, "cm"))

### FINAL PLOT: put box whisker plot in main plot
(final.gg <- g + annotation_custom(ggplotGrob(gg),  ymin=2.4, ymax=2.6))

您应该注意，ggplot 计算铰链的方法与 所使用的方法略有不同boxplot.stats。

# ggplot's hinges
bp = ggplot(data=df, aes(x=1, y=age)) + 
      geom_boxplot(outlier.shape=NA, size=1)
bpData = ggplot_build(bp)
bpData$data[[1]][1:5]