karyotype: karyotype plotting function

Description Usage Arguments Details Author(s) See Also

View source: R/karyotype.r

Description

A general overview of the whole genome of the sample.

Usage

1
karyotype(chr,start,end,int,ai,mchr,mpos,mval,schr,spos,sval,name='',xlim=c(0,2.5),ylim=c(0,1),MAPD=" ",MHOF=" ")

Arguments

chr

Chromosomes name of segs object. Final version of segs created from patchwork.Medians_n_AI().

start

Start position of segment.

end

End position of segment.

int

Normalized coverage.

ai

Allelic imbalance.

mchr

Chromosomes name of kbsegs object. Final version of kbsegs created from patchwork.smoothing().

mpos

Middle position of kbsegs segments.

mval

Ratio between kbsegs coverage and refcoverage.

schr

Chromosome names of alf object. Final version of alf created from patchwork.alleledata().

spos

Positions in alf.

sval

Inverse ratio between allele maximum and allele minimum.

name

Default is the name of the input BamFile from patchwork.plot(). Plot generated as "name_overview.jpg" in your working directory.

xlim

Default is c(0,2.5). Limit of x axis.

ylim

Default is 0:1. Limit of y axis.

MAPD

Placeholder for later sample measures.

MHOF

Placeholder for later sample measures.

Details

The plot is a overview, for a closer look see the plots generated by karyotype_chroms().

Walkthrough of the plot:

TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Normalized Coverage

The individual chromsomes in color plotted against the complete genome in grey.

TOP LOWER
Vertical axis: Normalized Coverage
Horizontal axis: Coordinate & Chromosome

Normalized coverage over coordinate for whole genome, chromosomally. See bottom for chromosome axis.

MIDDLE LOWER

Cytoband information for whole genome, chromosomally.

BOTTOM LOWER
Vertical axis: Allelic Imbalance
Horizontal axis: Coordinate & Chromosome

Allelic imbalance over coordinate for whole genome, chromosomally.

Author(s)

Markus Mayrhofer, [email protected].se Sebastian DiLorenzo, [email protected]

See Also

patchwork.plot
karyotype_chroms


xu-chang/patchwork-lite documentation built on March 19, 2018, 3:09 a.m.