Great fit ggplot2

Question

I want to build a limited cubic spline as the main plot and add a graph of squares and a mustache to show the change in the variable X. However, the lower hinge (x = 42), the median (x = 51) and the upper hinge (x = 61) did not perfectly match the corresponding grid lines of the main chart.

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)) 

• What do I need to change for a perfect fit?
• Is box-shaped mustache better for automated alignment of y-position?

UPDATE # 1 Thanks for your reply! Below you can see my example with your code. However, as you can see, the lower hinge, median and upper hinge are still not suitable. What is going wrong?

 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

Minor change: upgrade to ggplot2 2.0.0 axis.ticks.margin deprecated

In the boxplot field, even if you set the various elements in element_blank and the fields to zero, by default spaces remain as a result of misalignment. These spaces belong to:

• axis.ticks.length
• xlab

In the code below, I changed the code a bit (I hope everything is fine) and commented on some lines of code so that you can see that both graphs are aligned. I also set breaks on two graphs to round breaks (minimum and maximum values, hinges and median).

 # 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)) 

It should be noted that the ggplot method for calculating hinges is slightly different from the method used by boxplot.stats .

 # ggplot 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] 

Answer 2

An alternative answer using gtable functions to place a rectangle outside the main chart. Window graph height can be adjusted using parameter "h"

 library(rms) # Data 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) # X-axis breaks <- boxplot.stats(p[,"age"])$stats # Main plot MP <- ggplot(data=df, aes(x=age, y=yhat)) + geom_line(size=1) + geom_ribbon(data=df, aes(ymin=lower, ymax=upper), alpha=0.5, linetype=0, fill='#FFC000') + theme_bw() + scale_x_continuous(breaks=breaks) + xlab("Age") + ylab("Hazard Ratio") + theme(axis.line = element_line(color='black', size=1), axis.ticks = element_line(color='black', size=1), panel.grid.minor = element_blank()) # Boxplot BP <- ggplot(data=df, aes(x=factor(1), y=age)) + geom_boxplot(width = 1, outlier.shape=NA, size=1) + geom_jitter(position = position_jitter(width = .3), size = 1) + scale_y_continuous(breaks=breaks) + coord_flip() + theme_bw() + theme(panel.border=element_blank(), panel.grid=element_blank()) #### Set up the grobs and gtables here library(gtable) library(grid) h = 1/15 # height of boxplot panel relative to main plot panel # Get ggplot grobs gMP = ggplotGrob(MP) BPg = ggplotGrob(BP) BPg = gtable_filter(BPg, "panel") # from the boxplot, extract the panel only # In the main plot, get position of panel in the layout pos = gMP$layout[gMP$layout$name == "panel", c('t', 'l')] # In main plot, set height for boxplot gMP$heights[pos$t-2] = unit(h, "null") # Add boxplot to main plot gMP = gtable_add_grob(gMP, BPg, t=pos$t-2, l=pos$l) # Add small space gMP$heights[pos$t-1] = unit(5, "pt") # Draw it grid.newpage() grid.draw(gMP)