GenoView (version 1.6.0)

mutExonPlot: Mutations-Over-Exons Plot

Description

Superimpose user specified mutation data on the exons of a gene, with domain and legend annotations

Usage

mutExonPlot(mut.gr, exon.int, plot.int = exon.int, 
disp.track = 2, p.height = 1/4, d.height = 0, l.height = 1/2, 
plt.title = "mutExonPlot", id.col = "Fill", tx.db = NULL, pfam.gr = NULL, 
pfam.desc = NULL, pfam.ids = NULL, gr = NULL, ...)

Arguments

mut.gr

GRanges object containing mutation data, with fill values for legend if applicable

exon.int

GRanges object of length 1 of the genomic interval in which to count exons

plot.int

GRanges object of length 1 of the plotting interval in genomic coordinates

disp.track

Selects exon plotting track: 1 for full transcripts, 2 for reduced track

p.height

Numeric height allocation of Mutations-Over-Exons section in final grob

d.height

Numeric height allocation of domain annotation section in final grob

l.height

Numeric height allocation of legend section in final grob

plt.title

Plot title

id.col

Column containing identifiers in the values of mut.gr. It is only relevant in plotting a legend.

tx.db

TrancscriptDb object

pfam.gr

GRanges object of protein domain coordinates and Associated identifications

pfam.desc

list of PFAM definitions with Accession numbers

pfam.ids

character vector of Associated identifications with Accession numbers as names

gr

GRanges object containing genomic data (cds, utr, gap, intron, exon) over exon.int

...

Objects passed from the interface function if applicable

Value

Some elements may not be returned, depending on the chosen plot components.

mep

Mutations-Over-Exons final plot grob

plot

Mutations-Over-Exons component grob

domain

Domain component grob

legend

Legend component grob

show.domain

show.domain boolean

gr

GRanges object containing genomic data (cds, utr, gap, intron, exon) over exon.int

exon.int

GRanges object of length 1 which specifies the gene's genomic coordinates

If plotting fails, FALSE is returned.

Examples

## Not run: 
# library(TxDb.Hsapiens.UCSC.hg19.knownGene)
# library(biovizBase)
# 
# # Determine the published genomic datasets
# tx.db <- TxDb.Hsapiens.UCSC.hg19.knownGene
# data(genesymbol, package = "biovizBase")
# 
# # Create a mutation dataset in TP53
# exon.int <- genesymbol["TP53"]
# set.seed(2)
# N = 10
# mut.gr <- GRanges(seqnames = "chr17", 
#                     IRanges(start = sample(7575000:7580000, 
#                             size = N, replace = TRUE), 
#                             width = 1), 
#                     strand = "-")
# 
# mutExonPlot(mut.gr = mut.gr, exon.int = exon.int, l.height = 0, tx.db = tx.db)
# ## End(Not run)