I can not find a solution for my overplotting problem. If somebody could help me find a solution I would appreciate that a lot.
My data look like this (csv format): http://pastebin.com/embed_js.php?i=Cnfpkjsz
This is the code I am running:
library(dplyr)
library(gdata)
library(ggplot2)
library(directlabels)
all<-read.xls('all_auto_bio_adjusted.xls')
all$station<-as.factor(all$station)
all$automatic<-log(all$automatic)
all$averagebiol<-log(all$averagebiol)
all$stdevbiol<-log(all$stdevbiol)
pd <- position_dodge(.9)
allp<-ggplot(data=all, aes(y=averagebiol, x=automatic, colour=group)) +
geom_errorbar(aes(ymin=averagebiol-stdevbiol, ymax=averagebiol+stdevbiol), colour="red", width=.1, position=pd) +
geom_point(aes(size=size), show_guide = TRUE) +
geom_abline(intercept=0, slope=1) +
stat_smooth(method="loess",se=FALSE,colour='blue') +
geom_dl(aes(label=shortname),method="last.bumpup",cex = 1.3, hjust = 1) +
facet_wrap(~station,nrow=2)+
xlab("auto") +
ylab("manual") +
ggtitle("Comparison of automatic vs manual identification") +
scale_y_continuous(limits=c(0, max(all$averagebiol + all$stdevbiol))) +
theme_bw() +
theme(plot.title = element_text(lineheight=.8, face="bold", size=20,vjust=1), axis.text.x = element_text(colour="grey20",size=15,angle=0,hjust=.5,vjust=.5,face="bold"), axis.text.y = element_text(colour="grey20",size=15,angle=0,hjust=1,vjust=0,face="bold"), axis.title.x = element_text(colour="grey20",size=20,angle=0,hjust=.5,vjust=0,face="bold"), axis.title.y = element_text(colour="grey20",size=20,angle=90,hjust=.5,vjust=1,face="bold"),legend.position="right")
allp
I tried around quite a bit with different geom_dl methods but can’t find the right one. Is there one that can plot above the error bars?
If there is no good one for me. What could I do to at least have the labels plotted nicely so that I can rearrange them myself in photoshop?
Thanks a lot for your input!
3
Answers
Indeed I ended up faceting by station and group after input from Harrop.
Here is my code (The underlying data changed slightly)
I’m not familiar with
directlabels
but if you want to move the labels to the top you could just do it withgeom_text()
:However still seems too busy to distinguish between the groups. How about skipping the text labels and facetting over
station
andgroup
? Here’s a possible start, if you like it you would need to tune it…I hope you wanted somehting like this.
My code:
I removed your line of code for the labels and I introduced this one:
This is just putting the labels on top of the Error bar, with a small adjustment.
Also I modified this part:
With the labels on top, some of the labels where covered by the gray bar, so I increased a bit the value of the X bar (
+1
), but the max didn’t want to work correctly with my little addition, so I had to remove the NA values.