Ana Marija
2020-Jun-10 18:13 UTC
[R] Error in plot.window(...) : need finite 'ylim' values
Hello,
I do have a file like this:
head M3.assoc.logistic.C
CHR SNP BP P
1 1:785989:T:C 785989 0.4544
1 1:785989:T:C 785989 0.689
1 1:1130727:A:C 1130727 0.05068
1 1:1130727:A:C 1130727 0.07381
1 1:1156131:T:C 1156131 0.6008
1 1:1156131:T:C 1156131 0.8685
...
And I don't have any "NA" or "inf" values in it
and I am plotting it in R via:
library(qqman)
results_log <- read.table("M3.assoc.logistic.C", head=TRUE)
jpeg("Logistic_manhattan_retinopathy_M3.jpeg")
manhattan(results_log,chr="CHR",bp="BP",p="P",snp="SNP",
main "Manhattan plot: logistic")
dev.off()
but I am getting:
Error in plot.window(...) : need finite 'ylim' values
Calls: manhattan ... do.call -> plot -> plot.default -> localWindow
->
plot.window
Execution halted
Please advise,
Thanks
Ana
Hi Ana, I don't have the qqman package, but is your "P" column in "M3.assoc.logistic.C" numeric or has it been read in as a factor? Jim On Thu, Jun 11, 2020 at 4:13 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:> > Hello, > > I do have a file like this: > head M3.assoc.logistic.C > CHR SNP BP P > 1 1:785989:T:C 785989 0.4544 > 1 1:785989:T:C 785989 0.689 > 1 1:1130727:A:C 1130727 0.05068 > 1 1:1130727:A:C 1130727 0.07381 > 1 1:1156131:T:C 1156131 0.6008 > 1 1:1156131:T:C 1156131 0.8685 > ... > > And I don't have any "NA" or "inf" values in it > > and I am plotting it in R via: > > library(qqman) > results_log <- read.table("M3.assoc.logistic.C", head=TRUE) > jpeg("Logistic_manhattan_retinopathy_M3.jpeg") > manhattan(results_log,chr="CHR",bp="BP",p="P",snp="SNP", main > "Manhattan plot: logistic") > dev.off() > > but I am getting: > > Error in plot.window(...) : need finite 'ylim' values > Calls: manhattan ... do.call -> plot -> plot.default -> localWindow -> > plot.window > Execution halted > > Please advise, > > Thanks > Ana > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.