search

YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
499 stars 111 forks source link

Error in p values should be at range of (0, 1). #124

Open Liny2333 opened 2 months ago

Liny2333 commented 2 months ago

Can you please help me understanding the error thrown by CMplot? There is my code: data2<-read.table('newdata_1-6', head=TRUE) data2<-data2[order(data2[,2]),] library(CMplot) CMplot(data2,plot.type="c", r=0.4,col=c("grey30","grey60"), chr.labels=paste("Chr",c(1:6),sep=""), threshold=c(1e-6,1e-4),cir.chr.h=1.5, amplify=TRUE,threshold.lty=c(1,2), threshold.col=c("red","blue"),signal.line=1, signal.col=c("red","green"), chr.den.col=c("darkgreen","yellow","red"), bin.size=1e6,outward=FALSE,file="pdf", dpi=300,file.output=TRUE,verbose=TRUE) My data have the '0' values and I wonder if Manhattan can't be mapped with a p-value of zero.

Liny2333 commented 2 months ago
1715150444706
Liny2333 commented 2 months ago

And the error is Error in CMplot(data2, plot.type = "c", r = 0.4, col = c("grey30", "grey60"), : p values should be at range of (0, 1).

Liny2333 commented 2 months ago

I also try to use the other data which without a p-value of zero and i 've got the plot.How can I use data with a value of 0 to draw a circular Manhattan plot?