humarray (version 1.2)

plotGeneAnnot: Plot genes to annotate figures with genomic axes

Description

Quite often it is helpful to visualize genomic locations in the context of Genes in the same region. This function makes it simple to overlay genes on plots where the x-axis is chromosomal location.

Usage

plotGeneAnnot(chr = 1, scl = c("b", "kb", "mb", "gb"), y.ofs = 0,
  width = NA, txt = T, chr.pos.offset = 0, gs = NULL, build = NULL,
  dir = NULL, box.col = "green", txt.col = "black", join.col = "red",
  ...)

Arguments

chr

chromosome number/name that the plot-range lies on

scl

character, the scale that the x axis uses, ie, "b","kb","mb", or "gb", meaning base-pairs, kilobases, megabases or gigabase-pairs.

y.ofs

numeric, y-axis-offset, depending on what units are on your y-axis, you may prefer to specify an offset so that the gene annotation is drawn at an appropriate level on the vertical axis, this value should be the centre of annotation

width

depending on the range of your y-axis, you might want to expand or reduce the vertical width of the gene annotation (in normal graph units), default when width=NA is 10 percent of the y-axis size.

txt

logical, TRUE to include the names of genes on top of their representation on the plot, or if FALSE, genes are drawn without labels.

chr.pos.offset

if for some reason zero on the x-axis is not equal to 'zero' on the chromsome, then this offset can correct the offset. For instance if you were using a graph of the whole genome and you were plotting genes on chromosome 10, you would set this offset to the combined lengths of chromosomes 1-9 to get the start point in the correct place.

gs

GRanges or RangedData object, this is annotation for the location of genes. This will be retrieved using get.gene.annot() if 'gs' is NULL. THere may be several reasons for passing an object directly to 'gs'; firstly speed, if making many calls then you won't need to load the annotation every time; secondly, if you want to use an alternative annotation you can create your own so long as it is a GRanges/RangedData object and contains a column called 'gene' (which doesn't strictly have to contain gene labels, it could be any feature you require, eg., transcript names, etc).

build

string, currently 'hg18' or 'hg19' to specify which annotation version to use. Default is build-36/hg-18. Will also accept integers 36,37 as alternative arguments.

dir

character, location to store file with the gene annotation. If NULL then getOption("save.annot.in.current")>=1 will result in this file being stored in the current directory, or if <=0, then this file will not be stored.

box.col

genes are drawn as boxes, this sets the colour of the boxes

txt.col

this sets the colour of the label text (Gene names)

join.col

for exons, or multipart genes, joins are made between the sections with a central line, this sets the colour of that line.

...

further arguments to 'rect', the graphics function used to plot the 'genes'.

Value

Returns a data.frame, GRanges or RangedData object, depending on input parameters. Contained will be HGNC gene labels, chromosome and start and end positions, other information depends on specific parameters documented above

Examples

# NOT RUN {
# EXAMPLE PLOT OF SOME SIMULATED SNPS on chr21-p11.1 #
# do we need to require(GenomicRanges)? #
setwd(tempdir())
loc <- c(9.9,10.2)
Band(chr=21,pos=loc*10^6)
rr <- in.window(rranges(50000),chr=21,pos=loc,unit="mb") # make some random MHC ranges
# create some SNPs and plot
rr3 <- rr; end(rr3) <- start(rr3) 
rownames(rr3) <- paste0("rs",sample(10^6,nrow(rr3)))
plotRanges(rr3,col="blue",scl="mb",xlim=loc,xlab="Chr21 position (Mb)",ylab="")
# NOW add UCSC hg18 GENE annotation to the plot #
# }
# NOT RUN {
 plotGeneAnnot(chr=21,pos=c(9.95,10.1),scl="mb",y.ofs=1,build=36) 
# }