Entering edit mode
11.3 years ago
paulr
▴
80
Dear all, So I'm trying to use autoplot from the Bioconductor ggbio package. For some reason, the following data and code causes an odd error.
library(ggbio)
data(hg19IdeogramCyto, package = "biovizBase")
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
sample.data <- data.frame(chromosome='chr7', begin= 6018314, end= 6018316)
actual.var <- GRanges(seqnames=sample.data$chromosome, IRanges(start=sample.data$begin, end=sample.data$end))
p.2 <- autoplot(txdb, which = actual.var, color='blue', names.expr = "gene_id:::tx_name")
And here's the output and subsequent error
Aggregating TranscriptDb...
Parsing exons...
Parsing cds...
Parsing transcripts...
Aggregating...
Done
Constructing graphics...
Error in approx(c(x.s, x.e), rep(0, 2), n = N) :
negative length vectors are not allowed
Does GRanges require at least two coordinates? I just want to indicate where a small variant occurs.
Thanks in advance!