ggplot2 should work (resize to get the plot to the dimensions you need for the
paper)
library(Hmisc)
library(pscl)
library(ggplot2)
## data
data("bioChemists", package = "pscl")
fm_pois <- glm(art ~ ., data = bioChemists, family = poisson)
summary(fm_pois)
### pull out rate-ratios and 95% CI
rr <- exp(cbind(coef(fm_pois), confint(fm_pois)))
rr
### round to 2 decimal places
rr <- as.data.frame(round(rr, 2))
colnames(rr)<-c("y","ymin","ymax")
rr$labl<-rownames(rr) ## Change this to meaningful labels
rr$x<-1:length(rownames(rr))
gpl<-ggplot(rr,aes(x,y,ymin=ymin,ymax=ymax))
gpl+geom_point()+geom_linerange()+
geom_hline(aes(yintercept=1),
linetype="dashed",size=0.5)+
geom_text(aes(x,y=0.3,label=y,hjust=0),size=3)+
geom_text(aes(x,y=0.0,label=labl),size=3)+
geom_text(aes(x,y=0.5,label=paste("[",ymin,",",ymax,"]",sep="")
,hjust=0.0),size=3)+
ylab("Relative Risk")+xlab("")+
coord_cartesian(ylim=c(-1,1.7))+
coord_cartesian(xlim=c(0.85,6.15))+
scale_x_continuous(breaks=NA)+
scale_y_continuous(breaks=seq(0.8,1.6,.1))+
opts(
panel.grid.major = theme_blank(),
panel.grid.minor=theme_blank(),
title="",
panel.background = theme_rect(fill=NA,colour=NA)
)+
coord_flip()+
geom_text(aes(x=6.3,y=0.35,label="RR"),size=4)+
geom_text(aes(x=6.3,y=0.60,label="95% CI"),size=4)
Christos
> Date: Mon, 19 Apr 2010 09:29:48 -0700
> From: datk...@u.washington.edu
> To: r-help@r-project.org
> Subject: [R] plotting RR, 95% CI as table and figure in same plot
>
>
> Hi all--
>
> I am in the process of helping colleagues write up a ms in which we fit
> zero-inflated Poisson models. I would prefer plotting the rate ratios
> and 95% CI (as I've found Gelman and others convincing about plotting
> tables...), but our journals usually like the numbers themselves.
>
> Thus, I'm looking at a recent JAMA article in which both numbers and
> dotplot of RR and 95% CI are presented and wondering about best way to
> do this in R.
>
> Essentially, the plot has 3 columns: variable names, RR and 95% CI, and
> dotplot of the same.
>
> Using the bioChemists data in the pscl package and errbar function in
> Hmisc package, the code below is in the right direction... but still
> pretty ugly.
>
> Wondering if folks would have alternative suggestions about how to go
> about this, or pointers on cleaning up the code below (eg, I know there
> are many functions for plotting errbars/CI).
>
> [And, obviously, there are somethings that would be straightforward to
> clean-up such as supplying better variable names, etc., just wanted to
> see if there were better overall suggestions before getting too far on
> this route.]
>
> Thanks in advance.
>
> cheers, Dave
>
> library(Hmisc)
> library(pscl)
>
> ## data
> data("bioChemists", package = "pscl")
> fm_pois <- glm(art ~ ., data = bioChemists, family = poisson)
> summary(fm_pois)
>
> ### pull out rate-ratios and 95% CI
> rr <- exp(cbind(coef(fm_pois), confint(fm_pois)))
> rr
> ### round to 2 decimal places
> rr <- round(rr, 2)
>
> ### plot
> par(mfrow=c(1,3))
> plot(0, type = "n", xlim=c(0,2), ylim=c(1,6),
> axes = FALSE, ylab=NULL, xlab=NULL)
> text(row.names(rr), x = 1, y = 1:6)
>
> plot(0, type = "n", xlim=c(0,2), ylim=c(1,6),
> axes = FALSE, ylab=NULL, xlab=NULL)
> text(paste(rr[,1], " [", rr[,2], ", ", rr[,3], "]", sep = ""), x = 1, y
> = 1:6)
>
> errbar(x = factor(row.names(rr)),
> y = rr[,1], yplus = rr[,3],
> yminus = rr[,2])
> abline(v = 1, lty =2)
>
> --
> Dave Atkins, PhD
> Research Associate Professor
> Department of Psychiatry and Behavioral Science
> University of Washington
> datk...@u.washington.edu
>
> Center for the Study of Health and Risk Behaviors (CSHRB)
> 1100 NE 45th Street, Suite 300
> Seattle, WA 98105
> 206-616-3879
> http://depts.washington.edu/cshrb/
> (Mon-Wed)
>
> Center for Healthcare Improvement, for Addictions, Mental Illness,
> Medically Vulnerable Populations (CHAMMP)
> 325 9th Avenue, 2HH-15
> Box 359911
> Seattle, WA 98104?
> 206-897-4210
> http://www.chammp.org
> (Thurs)
>
> ______________________________________________
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