library("Gviz")
gen <- "hg19"
chr <- "chr15"
start <- 75011669
end <- 75019876
interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good"))
interestcolor <- list("bad"="red", "good"="green")
if(interactive()) {
interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,interestfeatures,interestcolor,showId=TRUE)
plotTracks(interestgenesENSMBLtrack, from = start, to =end)
} else {
data(interestgenesENSMBLtrack)
plotTracks(interestgenesENSMBLtrack, from = start, to =end)
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(coMET)
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych
Attaching package: 'psych'
The following object is masked from 'package:IRanges':
reflect
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coMET/interestGenes_ENSEMBL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: interestGenes_ENSEMBL
> ### Title: Create one track of the genes in the genomic regions of interest
> ### from EMSEMBL
> ### Aliases: interestGenes_ENSEMBL
> ### Keywords: hplot
>
> ### ** Examples
>
> library("Gviz")
> gen <- "hg19"
> chr <- "chr15"
> start <- 75011669
> end <- 75019876
> interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good"))
> interestcolor <- list("bad"="red", "good"="green")
>
> #if(interactive()) {
> interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,interestfeatures,interestcolor,showId=TRUE)
Warning message:
In .local(x, ..., na.rm = na.rm) : 'na.rm' argument is ignored
> plotTracks(interestgenesENSMBLtrack, from = start, to =end)
> } else {
Error: unexpected '}' in "}"
Execution halted