sv.model.view: SV integrated visualization

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Integrated visualization of SVC and CNV data for defined genomic locations. CNV and SVC data is overlayed into a sample-based track visualization map.

Usage

sv.model.view(
  cnv,
  svc,
  chrom,
  start,
  stop,
  sampleids = NULL,
  cnvlim = c(-2, 2),
  addlegend = "both",
  cex.legend = 1,
  interval = NULL,
  addtext = NULL,
  cex.text = 0.8,
  plot = TRUE,
  summary = TRUE,
  ...
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized by validate.cnv
svc	(S4) an object of class svcnvio containing data type 'svc' initialized by validate.svc
chrom	(character) chromosome (e.g chr9)
start	(numeric) genomic coordinate from specified chromosome to start plotting
stop	(numeric) genomic coordinate from specified chromosome to stop plotting
sampleids	(character) a vector containing a list of sample ids represented in svc and/or cnv objects to be plotted
cnvlim	(numeric) limits for color coding of background CNV log-ratios. Use to modify the CNV color contrast at different levels.
addlegend	(character) One of 'sv' (show SV type legend), 'cnv' (show CNV background color legend) or 'both'.
cex.legend	(numeric) The cex values for each legend
interval	(numeric) The axis interval in base pairs
addtext	(character) a vector indicating what SV types should include text labels indicating brakpoint partners genomic locations. The added labels are point breakpoint locations outside the plot area. (e.g. c("TRA","INV") )
cex.text	(numeric) The magnification to be used for SV text info added
plot	(logic) whether to produce a graphical output
summary	(logic) whether the function shoud return CNV segment 'segbrk' and SV 'svbrk' breakpoints tabular output
...	additional plot parameters from graphics plot function

Value

a data.frame with CNV and SVN breakpoint annotations and/or plot into open device

Examples

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)
svc <- validate.svc(svdat_lung_ccle)

# obtain the coordinates of a desired genomic regionbased on a known gene locus 
refSeqGene <- gene.symbol.info(refseq_hg19,"PTPRD")
start <- refSeqGene$start - 150000;
stop <- refSeqGene$stop+ 50000;
chrom <- refSeqGene$chrom

sv.model.view(cnv, svc, chrom, start, stop)

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.