karyotype_chroms: Karyotype plotting of each chromosome

Description Usage Arguments Details Author(s) See Also

View source: R/karyotype_chroms.r

Description

Visualises the calculated data of patchwork.plot() for each chromosome. See details for a walkthrough of the plot.

Usage

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

Name of sample. patchwork.plot sends it as name of the bamfile.

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

Walkthrough of the plot:

TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Normalized coverage

The chromosome plotted against the complete genome background. The separation between clusters within the plot are due to the fluctuating coverage and allelic imbalance and as such display the varying allele counts and copy numbers. Longer/larger segments have bigger circles. Darker circles show more content as they are ontop of eachother.

MIDDLE
Vertical axis: Normalized coverage
Horizontal axis: Position (Mb)

The chromosome in questions normalized coverage plotted against the position on the chromosome.

CYTOBAND

Cytoband information for selected chromosome.

BOTTOM
Vertical axis: Allelic imbalance
Horizontal axis: Position (Mb)

The chromosome in questions allelic imbalance plotted against the position on the chromosome.

Author(s)

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

See Also

patchwork.plot
karyotype


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