YinLiLin
Error : missing value where TRUE/FALSE needed
Can you please help me understanding the error thrown by CMplot?
Error in if ((y[i] + 1.5 * strheight(words[i], cex = text.cex)) > max(ylim)) { : missing value where TRUE/FALSE needed
My code,
`length_ds<-read_csv("Length_control.csv") Highlight_SNPs<-read.csv("Highligting_SNPs.csv", header = T)
CMplot(length_ds, plot.type="m",LOG10=TRUE,col=c("grey30","grey60"),highlight=Highlight_SNPs$SNP,
highlight.col=c("red","blue","green"),highlight.cex=1,highlight.pch=c(15:17), highlight.text=Highlight_SNPs$Gene,
highlight.text.col=c("red","blue","green"),threshold=0.5/nrow(length_ds),threshold.lty=2,
amplify=FALSE,file="jpg",memo="",dpi=300,file.output=TRUE,verbose=TRUE,width=14,height=6)
`
Highliting_SNPs.csv looks like,
| SNP | Gene |
|---|---|
| SNP-1.2550305. | GeneA1 |
| SNP-1.18463769. | GeneA2 |
| SNP-1.31315134. | GeneA3 |
| SNP-1.31712331. | GeneA4 |
| SNP-1.31874931. | GeneA5 |
| SNP-1.31894544. | GeneA6 |
Please note that Manhattan plot without gene highlighting works with my input dataset (4 columns :marker, chrome,pos, and trait). So I guess it has something to do with highlighting file or format.
It seems that the format of all the data you prepared looks fine, would you mind sending me your data? i am pleasure to debug the problem and feed back to you soon.
Hi, I have located the problem that caused the error you proposed. As CMplot will force the p-value to be in range of 0-1, any digits out of this range will be replaced by NA, if p-value of the highlighted SNP is in this case, it cannot be displayed, because it has no y position, please check your data, and find out why the p-values of some SNPs are bigger than 1.