Introduction
This package was first designed to set breakpoints for truncating theplot as I need toshrinkoutlier long branch of a phylogenetic tree.
Axis break or a so call gap plot is useful for large datasets thatare not normally distributed and contain outliers. Sometimes we cantransform the data (e.g. using log-transformation if the data waslog-normal distributed) to solve this problem. But this is not alwaysgranted. The data may just simply contain outliers and these outliersare meaningful. A simple gap plot can solve this issue well to presentthe data in detail with both normal and extreme data.
This package provides several scale functions to break down a ‘gg’plot into pieces and align them together with (gap plot) or without(wrap plot or cut plot) ignoring subplots. Our methods are fullycompatible withggplot2, so that users can still use the+ operator to add geometric layers after creating a brokenaxis.
If you useggbreak inpublished research, please cite the following paper:
- S Xu#, M Chen#, T Feng, L Zhan, L Zhou,G Yu*. Use ggbreak to effectively utilizeplotting space to deal with large datasets and outliers.Frontiers in Genetics. 2021, 12:774846. doi:10.3389/fgene.2021.774846
Gap plot
For creating gap plot, we only providescale_x_break andscale_y_break functions. Currently, it is not allowed toapply both functions to set breakpoints for both x and y axes. However,multiple breakpoints on a single axis are supported.
Feature 1: Compatible with ggplot2.
After breaking the plot, we can still superpose geometric layers andset themes.
library(ggplot2)library(ggbreak)library(patchwork)set.seed(2019-01-19)d<-data.frame(x =1:20,y =c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22))p1<-ggplot(d,aes(y, x))+geom_col(orientation="y")d2<-data.frame(x =c(2,18),y =c(7,26),label =c("hello","world"))p2<- p1+scale_x_break(c(7,17))+geom_text(aes(y, x,label=label),data=d2,hjust=1,colour ='firebrick')+xlab(NULL)+ylab(NULL)+theme_minimal()p1+ p2Feature 3: Zoom in or zoom out of subplots
Feature 4: Support reverse scale
g<-ggplot(d,aes(x, y))+geom_col()g2<- g+scale_y_break(c(7,17),scales =1.5)+scale_y_break(c(18,21),scale=2)+scale_y_reverse()g+ g2Feature 5: Compatible with scale transform functions
Users can apply scale transform functions, such asscale_x_log10 andscale_x_sqrt, to axis breakplot.
Feature 7: Compatible withfacet_grid andfacet_wrap
set.seed(2019-01-19)d<-data.frame(x =1:20,y =c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22),group =c(rep("A",10),rep("B",10)),face=c(rep("C",5),rep("D",5),rep("E",5),rep("F",5)))p<-ggplot(d,aes(x=x,y=y))+geom_col(orientation="x")+scale_y_reverse()+facet_wrap(group~.,scales="free_y",strip.position="right",nrow=2 )+coord_flip()pg<- p+scale_y_break(c(7,17),scales="free")+scale_y_break(c(19,21),scales="free")print(pg)Feature 9: Supports all plot labels
pg+labs(title="test title",subtitle="test subtitle",tag="A tag",caption="A caption")+theme_bw()+theme(legend.position ="bottom",strip.placement ="outside",axis.title.x=element_text(size=10),plot.title =element_text(size =22),plot.subtitle =element_text(size =16),plot.tag =element_text(size =10),plot.title.position ="plot",plot.tag.position ="topright",plot.caption =element_text(face="bold.italic"), )Feature 10: Allows setting tick labels for subplots
require(ggplot2)library(ggbreak)set.seed(2019-01-19)d<-data.frame(x =1:20,y =c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22),group =c(rep("A",10),rep("B",10)))p<-ggplot(d,aes(x=x,y=y))+scale_y_reverse()+scale_x_reverse()+geom_col(aes(fill=group))+scale_fill_manual(values=c("#00AED7","#009E73"))+facet_wrap( group~.,scales="free_y",strip.position="right",nrow=2 )+coord_flip()p+scale_y_break(c(7,10),scales=0.5,ticklabels=c(10,11.5,13))+scale_y_break(c(13,17),scales=0.5,ticklabels=c(17,18,19))+scale_y_break(c(19,21),scales=1,ticklabels=c(21,22,23))Feature 11: Compatible with dual axis
p<-ggplot(mpg,aes(displ, hwy))+geom_point()+scale_y_continuous("mpg (US)",sec.axis =sec_axis(~ .*1.20,name ="mpg (UK)") )+theme(axis.title.y.left =element_text(color="deepskyblue"),axis.title.y.right =element_text(color ="orange") )p1<- p+scale_y_break(breaks =c(20,30))p2<- p+scale_x_break(breaks =c(3,4))p1+ p2Wrap plot
Thescale_wrap() function wraps a ‘gg’ plot overmultiple rows to make plots with long x-axes easier to read.
Both categorical and numerical variables are supported.
Cut plot
Thescale_x_cut orscale_y_cut cuts a ‘gg’plot to several slices with the ability to specify which subplots tozoom in or zoom out.
library(ggplot2)library(ggbreak)set.seed(2019-01-19)d<-data.frame(x =1:20,y =c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22) )p<-ggplot(d,aes(x, y))+geom_col()p+scale_y_cut(breaks=c(7,18),which=c(1,3),scales=c(3,0.5))Adjust the amount of space between subplots
Thespace parameter inscale_x_break(),scale_y_break(),scale_x_cut() andscale_y_cut() allows user to control the space betweensubplots.
Place legend at any position
## original plotp1<-ggplot(mpg,aes(displ, hwy,color=factor(cyl)))+geom_point()## ggbreak plot without legendp2<- p1+scale_x_break(c(3,4))+theme(legend.position="none")## extract legend from original plotleg= cowplot::get_legend(p1)## redraw the figurep3<- ggplotify::as.ggplot(print(p2))## place the legendp3+ ggimage::geom_subview(x=.9,y=.8,subview=leg)Note
The features we introduced forscale_x_break andscale_y_break also work forscale_wrap,scale_x_cut andscale_y_cut.
FAQ
- Incompatible with functions that arrange multiple plots
You can useaplot::plot_list() to arrangeggbreak objects with otherggplot objects. Forother functions, such ascowplot::plot_grid() andgridExtra::grid.arrange(), you need to explictly callprint() toggbreak object, see alsohttps://github.com/YuLab-SMU/ggbreak/issues/36.
Usingprint() is a secret magic to makeggbreak compatible with other packages, includingexport.