genomePlot: draw a genome plot

Description Usage Arguments Details Value Author(s) See Also Examples

Description

draw a genome plot with user defined genomic regions

Usage

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# genomePlot(.Object, genomicRegions=NULL, draw.blocks=TRUE,
# parallel.plot=TRUE, grouping=NULL, custom.labels=NULL,
#  scale.positions=NULL, qval.threshold=0.05,
# use.referencePositions=FALSE, smoothStatistic.tail=NULL,
# smoothStatistic.threshold=NULL, region.colors=NULL,
# limitChrs=NULL)

genomePlot(.Object, ...)

Arguments

.Object

Object of class GenomicAnnotationsForPREDA, or any other class exteinding this one.

...

See below

genomicRegions:

A list of GenomicRegions object containing the genomic regions to be highlighted in the plot.

draw.blocks:

If TRUE genomic regions are plotted as blocks. Otherwise they are plotted as coloured ticks. Currently only draw.blocks=TRUE is implemented.

parallel.plot:

Logical, if TRUE multiple copies of each chrosomosome are drawn.

In particular a number of copies equal to lnegth(grouping), if grouping is not null, or a number of copies equal to the number of GenomicRegions objects provided as input.

grouping:

Vector specifying how input GenomicRegions objects will be grouped on chromosomes.

custom.labels:

A character to specify user defined labels for vertical axis

scale.positions:

Parameter to set the scale for chromosomal positions (horizontal axis). Possible values are "Mb" or "Kb"

qval.threshold:

If genomicRegions is NULL, and a PREDAResults or PREDADataAndResults is provided as input, the function PREDAResults2GenomcRegions is applied with this parameter to extract significant GenomicRegions.

use.referencePositions:

If genomicRegions is NULL, and a PREDAResults or PREDADataAndResults is provided as input, the function PREDAResults2GenomcRegions is applied with this parameter to extract significant GenomicRegions.

smoothStatistic.tail:

If genomicRegions is NULL, and a PREDAResults or PREDADataAndResults is provided as input, the function PREDAResults2GenomcRegions is applied with this parameter to extract significant GenomicRegions.

smoothStatistic.threshold:

If genomicRegions is NULL, and a PREDAResults or PREDADataAndResults is provided as input, the function PREDAResults2GenomcRegions is applied with this parameter to extract significant GenomicRegions.

region.colors:

Character vector specifyin the list of colors to be used for drawing each set of GenomicRegions. Mut be of length equal to the number of GenomicRegions objects provided as input.

limitChrs:

Numeric vector, that can be used to limit the plot to a subset of chromosomes.

Details

See also the PREDA tutorial vignette for more details and sample usage

Value

A plot of the genome with significant GenomicRegions

Author(s)

Francesco Ferrari

See Also

PREDAResults2GenomicRegions, PREDAResults, PREDADataAndResults, GenomicAnnotationsForPREDA

Examples

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## See PREDA tutorial vignette for some examples

PREDA documentation built on May 6, 2019, 2:07 a.m.