[R] need help on forest plot with ggplot

[Brian Diggs]

On 9/29/2011 8:11 PM, wirichada wrote:
> Dear R users,
>
> I am trying to do the forest plot follow the function given on web. However,
> the order of the tests has been sorted alphabetically. I would prefer
> keeping the order as data frame input so that I can group and compare (from
> the graph) the target immune NS1, IgG and IgM (where SD, BioRad, Pb etc are
> the brand names)
>
>
>
>> d
>
>                      x        y      ylo      yhi
>
> SD.NS1         SD.NS1 43.23250 38.25736 48.20764
> BioRad.NS1 BioRad.NS1 57.31750 54.28494 60.35006
> Pb.NS1         Pb.NS1 56.21563 53.14092 59.29033
> SD.IgG         SD.IgG 62.26750 60.65677 63.87823
> Iq.IgG         Iq.IgG 78.80917 78.34625 79.27209
> Merlin.IgG Merlin.IgG 62.46333 60.68995 64.23672
> Pb.IgG         Pb.IgG 57.51500 56.94022 58.08978
> SD.IgM         SD.IgM 76.90417 75.61221 78.19613
> Iq.IgM         Iq.IgM 79.45917 78.73032 80.18801
> Merlin.IgM Merlin.IgM 64.50167 60.30376 68.69958
> Pb.IgM         Pb.IgM 65.38667 61.81591 68.95742
> AFRIMS         AFRIMS 88.29958 84.84922 91.74995
>
> I am currently using the code as suggested on web:
>
> credplot.gg<- function(d){require(ggplot2)
>
> p<-
> ggplot(d,aes(x=x,y=y,ymin=ylo,ymax=yhi))+geom_pointrange()+coord_flip()+
>
> xlab('RDT tests')+ylab('Sensitivity')
>
> return(p)}
>
> d<-
> data.frame(x=names(ragama.meta)[2:13],y=xx[2:13],ylo=xx[2:13]-1.96*ss[2:13],
>
> yhi=xx[2:13]+1.96*ss[2:13])
>
> credplot.gg(d)
>
>
>
> How should I correct this so that I can fix the order of the rapid tests the
> way I put in.

I'm assuming that d$x is a character.  If it is, ggplot turns it into a 
factor for plotting, which by default puts the values in alphabetical 
order.  If you make it into a factor with the levels in the order you 
want, ggplot will honor that.

d$x <- factor(d$x, levels=d$x)

> Thank you in advance.
>
> Wirichada (Pongtavornpinyo) Pan-ngum
> Mathematical Modelling team
> Mahidol-Oxford Tropical Medicine Research Unit (MORU)
> Faculty of Tropical Medicine, Mahidol University
> 420/6 Ratchawithi Rd., Bangkok 10400 Thailand
> Tel:  +66 2 203 6322
> Fax:  +66 2 354-9169
> Email: pan at tropmedres.ac
> http://r.789695.n4.nabble.com/file/n3858577/image001.png
>
> --
> View this message in context: http://r.789695.n4.nabble.com/need-help-on-forest-plot-with-ggplot-tp3858577p3858577.html
> Sent from the R help mailing list archive at Nabble.com.

-- 
Brian S. Diggs, PhD
Senior Research Associate, Department of Surgery
Oregon Health & Science University