plot.genomic: Plotting a section of a chromosome.

In annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Description

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

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).

Author(s)

Tim Yates

annmap documentation built on Nov. 8, 2020, 7:43 p.m.