genome.wide.plot {saasCNV} | R Documentation |
Visualize Genome-Wide SCNA Profile
Description
An optional function to visualize genome-wide SCNA Profile.
Usage
genome.wide.plot(data, segs, sample.id, chrs, cex = 0.3)
Arguments
data |
a data frame containing log2ratio and log2mBAF data generated
by |
segs |
a data frame containing segment location, summary statistics
and SCNA status resulting from |
sample.id |
sample ID to be displayed in the title of the plot. |
chrs |
the chromosomes to be visualized. For example, 1:22. |
cex |
a numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. It can be adjusted in order to make the plot legible. |
Details
On the top panel, the log2ratio signal is plotted against chromosomal position and on the panels blow, the log2mBAF, tumor mBAF, and normal mBAF signals. The dots, each representing a probe data point, are colored alternately to distinguish chromosomes. The segments, each representing a DNA segment resulting from the joint segmentation, are colored based on inferred copy number status.
Value
An R plot will be generated.
Author(s)
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
See Also
joint.segmentation
, cnv.call
,
diagnosis.seg.plot.chr
, diagnosis.cluster.plot
Examples
data(seq.data)
data(seq.cnv)
genome.wide.plot(data=seq.data, segs=seq.cnv,
sample.id="PT116",
chrs=sub("^chr","",unique(seq.cnv$chr)),
cex=0.3)