Dear all,
I encountered a problem when I plotted some genes with plotTracks using Gviz. It happened only to those genes with very large coordinates (end > 536870912) on the chromosome.
Listed here are a subset of my code, the error message, and sessionInfo(). Thank you for your help.
Suh-Yuen
S24<- AlignmentsTrack("SR19AA2418Aligned.sortedByCoord.out.bam", isPaired = TRUE, name="S24", col="sandybrown", fill="sandybrown", cex=0.8)
for (i in 12:length(targets)){ ID<-targets[i] start<-genemodel$start[genemodel$gene==ID & genemodel$feature=="mRNA"] end<-genemodel$end[genemodel$gene==ID & genemodel$feature=="mRNA"] chr<-genemodel$chr[genemodel$gene==ID & genemodel$feature=="mRNA"]
aTrack1 <- AnnotationTrack( genemodel[genemodel$chr==chr & genemodel$gene==ID & genemodel$feature=="CDS",], chromosome = chr, start = start, end = end, Id = ID, feature=ID, group = ID, name = "Gene Annotation", col="blue", fill="blue",cex=0.9 )
axisTrack <- GenomeAxisTrack(cex = 1,cex=0.9,exponent=5) # set the font size larger
grtrack <- GeneRegionTrack( genemodel[genemodel$chr==chr,], chromosome = chr, showId = TRUE, fontcolor="black",stacking="full", name = "Gene Annotation",col="grey", fill="grey",cex=1.2 )
fname<-paste0("P:/Assembly/ginkgo/P450s/Gviz/localginkgo",ID,"_",chr,"RNASeq.png") png(filename = fname,width =680, height = 680)
plotTracks(c(axisTrack, grtrack, aTrack1, S24),from=start,to=end,chromosome=chr, name=ID, type = "coverage",size=c(15,1,1,1),margin=2, shape="arrow", just.group = "above", transcriptAnnotation="gene", cex=1, extend.right=300, extend.left=300, cex.main=1.4, main=paste("RNASeq expression of", ID, "at", chr),title.width=1.5 )
dev.off() }
Error in value[3L] : 'end' must be <= 536870912 file: SR19AA2418Aligned.sortedByCoord.out.bam index: SR19AA2418Aligned.sortedByCoord.out.bam.bai In addition: There were 30 warnings (use warnings() to see them)
c(start,end,chr) [1] "689297194" "689298824" "Chr5"
sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)
Matrix products: default
Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding
locale:
[1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252
[3] LCMONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LCTIME=English_United States.1252
attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures1.38.2 AnnotationDbi1.48.0 Biobase2.46.0 Rsamtools2.2.2
[5] Biostrings2.54.0 XVector0.26.0 Gviz1.30.3 GenomicRanges1.38.0
[9] GenomeInfoDb1.22.0 IRanges2.20.2 S4Vectors0.24.3 BiocGenerics0.32.0
[13] openxlsx4.1.4 dplyr0.8.4
loaded via a namespace (and not attached):
[1] ProtGenerics1.18.0 bitops1.0-6 matrixStats0.55.0
[4] bit640.9-7 RColorBrewer1.1-2 progress1.2.2
[7] httr1.4.1 tools3.6.2 backports1.1.5
[10] R62.4.1 rpart4.1-15 Hmisc4.3-1
[13] DBI1.1.0 lazyeval0.2.2 colorspace1.4-1
[16] nnet7.3-12 tidyselect1.0.0 gridExtra2.3
[19] prettyunits1.1.1 bit1.1-15.2 curl4.3
[22] compiler3.6.2 htmlTable1.13.3 DelayedArray0.12.2
[25] rtracklayer1.46.0 scales1.1.0 checkmate2.0.0
[28] askpass1.1 rappdirs0.3.1 stringr1.4.0
[31] digest0.6.25 foreign0.8-75 dichromat2.0-0
[34] htmltools0.4.0 base64enc0.1-3 jpeg0.1-8.1
[37] pkgconfig2.0.3 ensembldb2.10.2 BSgenome1.54.0
[40] dbplyr1.4.2 htmlwidgets1.5.1 rlang0.4.4
[43] rstudioapi0.11 RSQLite2.2.0 BiocParallel1.20.1
[46] acepack1.4.1 zip2.0.4 VariantAnnotation1.32.0
[49] RCurl1.98-1.1 magrittr1.5 GenomeInfoDbData1.2.2
[52] Formula1.2-3 Matrix1.2-18 Rcpp1.0.3
[55] munsell0.5.0 lifecycle0.1.0 stringi1.4.6
[58] SummarizedExperiment1.16.1 zlibbioc1.32.0 BiocFileCache1.10.2
[61] blob1.2.1 crayon1.3.4 lattice0.20-40
[64] splines3.6.2 hms0.5.3 knitr1.28
[67] pillar1.4.3 biomaRt2.42.0 XML3.99-0.3
[70] glue1.3.1 biovizBase1.34.1 latticeExtra0.6-29
[73] data.table1.12.8 png0.1-7 vctrs0.2.3
[76] gtable0.3.0 openssl1.4.1 purrr0.3.3
[79] assertthat0.2.1 ggplot23.2.1 xfun0.12
[82] AnnotationFilter1.10.0 survival3.1-8 tibble2.1.3
[85] GenomicAlignments1.22.1 memoise1.1.0 cluster_2.1.0
Hi Robert, Thank you very much for your help! In that case, I would have to give up using Gviz. Suh-Yuen