Plot ENSEMBL genes

Plot ENSEMBL genes in region

Usage

plotEnsGenes(
  ensdb,
  wh,
  splice_variants = FALSE,
  non_coding = FALSE,
  arrow.size = 0.05,
  ensGene = NULL,
  size = 8
)

Arguments

ensdb

ENSEMBL database object like EnsDb.Hsapiens.v86

wh

genome interval to plot

splice_variants

if TRUE, show multiple transcripts from the same gene

non_coding

if TRUE, also show non-coding genes

arrow.size

arrow size for genes

ensGene

show specific non-coding locus

size

font size

Value

ggplot2 of genome region

Examples

library(EnsDb.Hsapiens.v86)
#> Error in library(EnsDb.Hsapiens.v86): there is no package called ‘EnsDb.Hsapiens.v86’
library(GenomicRanges) 
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb

# gene database
ensdb = EnsDb.Hsapiens.v86
#> Error: object 'EnsDb.Hsapiens.v86' not found

# interval
query = GRanges("20", IRanges(62045027,62164563))
#> Warning: 'S4Vectors:::anyMissing()' is deprecated.
#> Use 'anyNA()' instead.
#> See help("Deprecated")
#> Warning: 'S4Vectors:::anyMissing()' is deprecated.
#> Use 'anyNA()' instead.
#> See help("Deprecated")

# plot genes
plotEnsGenes( ensdb, query)
#> Warning: 'S4Vectors:::anyMissing()' is deprecated.
#> Use 'anyNA()' instead.
#> See help("Deprecated")
#> Warning: 'S4Vectors:::anyMissing()' is deprecated.
#> Use 'anyNA()' instead.
#> See help("Deprecated")
#> Error: object 'ensdb' not found