Error message when ploting with "R" - r
I am attempting to plot my dataset using PCA in R in Windows 10. But while plotting I got the message
zero-length 'labels' specified
Below are the data set and code:
Taxon,L/D1 ,L/D4,L/DL,Di.Pro.,ST,H.Fo/H.Ch
1,3,2.9,2.28,200,2,1
1,1.33,2.3,2.44,225,2,1
1,2,2.52,2.4,150,2,1
1,3.5,2.75,2.32,125,2,1
1,3.18,2.81,2,125,2,1
1,2.35,3,2.82,125,2,1
1,2.72,2.28,2.09,250,2,1
2,3.6,2.82,2.65,125,4,1
2,2.5,2.7,3.02,150,4,1
2,3.2,2.6,2.7,150,4,1
2,2.4,3.3,2.7,200,4,1
2,3,2.87,3.08,175,4,1
3,2,2.83,2,100,1,0.67
3,4,2.66,2.26,100,1,0.67
3,2.33,2.78,2.28,150,1,0.67
3,2,2.83,2.3,100,1,0.67
4,2.83,2.83,2.66,200,1,0.66
4,3.66,2.57,2.27,100,1,0.66
4,3.33,2.9,2.25,150,1,0.66
4,4.33,3.09,2.15,125,1,0.66
4,1.85,2.44,2.43,225,1,0.66
4,2.85,2.57,2.65,175,1,0.66
4,2.8,2.55,2.2,200,1,0.66
4,1.85,2.57,2.04,175,1,0.66
5,2.83,2.5,3,125,3,0.66
5,2.8,4,3.14,200,3,0.66
5,2,3.5,2.4,200,3,0.66
5,3,3.42,2.9,150,3,0.66
5,2.4,2.6,2.71,175,3,0.66
5,4,3.37,2.52,125,3,0.66
5,1.75,2.69,2.9,250,3,0.66
5,2,2.54,2.76,200,3,0.66
5,2.4,3.25,2.46,175,3,0.66
6,3.5,3.14,2.48,75,5,1
6,2.25,2.16,2.1,75,5,1
6,3,3.23,2.77,125,5,1
6,2.5,2.3,1.85,100,5,1
6,2.95,2.71,2.14,100,5,1
6,2.5,3.4,3.09,125,5,1
6,2,2.57,2.3,100,5,1
6,3,2.55,2.46,125,5,1
7,3,4.76,2.94,100,1,1
7,1.66,2.77,2.2,200,1,1
7,2.16,2.8,2.4,250,1,1
8,2.25,3.09,2.83,150,3,1
8,3.5,3.5,2.88,125,3,1
8,3.33,2.87,3.04,150,3,1
library(vegan)
daz= read.csv (file.choose())
cor(daz)
daz.pca<-rda(daz)
summary(daz.pca)
PCA1,2
daz.taxon.pca <- rda(daz[,c(2:7)],scale=T)
par(pty="s")
plot(scores(daz.taxon.pca,display="sites",choices=1),scores(daz.taxon.pca,display="sites",choices=2),type="n",xlab="PCA1 (99.69%)",ylab="PCA2 (0.19%)",xlim=c (-8.00,8.00),ylim=c(-2.00,1.50))
abline(v=0,lty=3)
abline(h=0,lty=3)
arrows(0,0,scores(daz.taxon.pca,display="species",choices=1),scores(daz.taxon.pca,display="species",choices=2),length=0.10,col="dark gray")
text(scores(daz.taxon.pca,display="sites",choices=1),scores(daz.taxon.pca,display="sites",choices=2),as.character(daz$taxon),cex=0.7)
Error in text.default(scores(daz.taxon.pca, display = "sites", choices
= 1), : zero-length 'labels' specified
Any help? I am rather new to R, and failed to find any explanation of this error. The code in general seems fine, except when I add
text(scores(daz.taxon.pca,display="sites",choices=1),scores(daz.taxon.pca,display="sites",choices=2),as.character(daz$taxon),cex=0.7)
for the plot, the error comes up. Any hint would be greatly appreciated.
You use daz$taxon instead of daz$Taxon to access the data in daz variable which return back NULL.
Use the following code at the end of your analysis and it should work fine:
text(scores(daz.taxon.pca, display="sites", choices=1),
scores(daz.taxon.pca, display="sites", choices=2),
as.character(daz$Taxon),
cex=0.7)
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In this case the error message seems to be misleading, at least to my reading. It appears to point to the error being in the call to survfit when in fact it's an error within ggsurvplot as can be seen from the output of traceback(). I first tried to change the name of the object passed to survival.function. Then no error. But also no plot. So also added a print call inside survival.function. I'll attache the first of the two plots that result.
survival.function<- function(data, datanames){
sfit<- survfit(Surv(surv.days, censor)~1, data=data)
print( ggsurvplot(sfit, conf.int=TRUE, risk.table=TRUE,
surv.median.line = "v",
title=datanames,
risk.table.height=.25) )
}
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Error in barplot.default(StandtM, main = "h2, c2, e2 by Mod FEMALES",
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In addition: Warning message:
In plot.window(xlim, ylim, log = log, ...) :
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I had the same error, then I noticed that I had made a variable called dist, which is the default call for distfun= dist. I renamed the variable and then everything ran fine. You likely made the same error, as your new code is working since you have altered the default call of distfun.
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A discussion I found online is helpful for adding customized text (e.g., basic statistics) on each of the histograms: https://stat.ethz.ch/pipermail/r-help/2007-March/126842.html