genomePlot {PREDA} | R Documentation |
draw a genome plot
Description
draw a genome plot with user defined genomic regions
Usage
# 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
## See PREDA tutorial vignette for some examples
[Package
PREDA version 1.30.0
Index]