Usage
genomicPlot( xrange, gene.area.height=NULL, gene.layout.padding=100, highlights=NULL, draw.opposite.strand=FALSE, exon.depth.plot=genomicExonDepthPlot, padding.lines=1, .genes=NULL, .exons=NULL, invert.strands=FALSE, draw.scale=TRUE, ... ) genomicExonDepthPlot( .exons, start, end, exon.depth.alpha=0.1, exon.depth.col='black', ... ) genomicProbePlot( probes, start, end, probe.col='green', probe.alpha=0.3, ... )
Arguments
xrange
An IRanges object representing the region of interest (with a strand if reqd)
gene.area.height
If NULL then both strands to max height of either of them, else if NA then both strands limited to their implied height otherwise, if an integer then both strands limited to the specified height
gene.layout.padding
How much space (in bases) needs to be between each gene in a layer. Needed to stop gene names overlapping
highlights
You can pass this a data.frame of values to render as dummy genes in the view. Columns MUST include start, end, strand and name. It may also optionally include the columns col to specify a per-gene background colour, or bor to specify the colour to be used for the gene border and the label text. If these two are not passed, sensible defaults are chosen automatically.
draw.opposite.strand
Do we draw a washed out representation of the other strand. Only applies if strand( xrange ) != '*'
exon.depth.plot
Should we draw the exondepth? set to NULL if not
padding.lines
How much padding above and below the plot (in grid lines)
.genes
Optionally pass in the pre-loaded genes and exons (then we skip loading them in this function)
.exons
The exons that are to be used
invert.strands
Should the forward strand be on the bottom of the plot?
draw.scale
Draw a scale between the two strands?
...
Parameters passed on to functions called by this function
exon.depth.alpha
The transparency for the exon.depth rectangles
exon.depth.col
The color for the exon.depth rectangles
start
The start of the region of interest
end
The end of the region of interest
probe.alpha
How transparent should probes be rendered?
probe.col
The colour to use for probes.
probes
The probes for the region of interest (as a data.frame).