Plotting a section of a chromosome.

Description

These functions are used when we need to plot one or both strands of a section of chromosome.

Usage

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  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).

Author(s)

Tim Yates