Karyotype plotting of each chromosome

Share:

Description

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

Usage

1
CG_KaCh(chr,start,end,int,ai,mchr,mpos,mval,sval,schr,spos,name,xlim,ylim)

Arguments

chr

Chromosomes name of segm object, as generated from somaticCnvSegmentsNonDiplod file.

start

Start position of segment.

end

End position of segment.

int

Ratio between relative coverage and segment length.

ai

Allelic imbalance as calculated from (1 - (lesser readcount / greater readcount)) per segment.

mchr

Chromosomes name of depcov (depthOfCoverage file).

mpos

Start position from depcov.

mval

Ratio between averagenormalizedcoverage and mean(averagenormalizedcoverage) from depthOfCoverage file.

sval

Inverse ratio between allele maximum and allele minimum per position.

schr

Chromosomes name of mastervar.

spos

Start position from mastervar.

name

Name that you want output to have. Default is ' ' which will yield files named as '_KaCh_chr#.png'. When method is run by patchwork.CG.plot() it will inherit the name parameter thereof.

xlim

Default is c(0,2.4). Limit of x axis for whole genome plot.

ylim

Default is c(0,1). Limit of y axis for whole genome plot.

Details

Walkthrough of the plot:

TOP
Vertical axis: Allelic Imbalance
Horizontal axis: Total Intensity

The chromosome plotted against the complete genome background. The separation between clusters within the plot are due to the fluctuating intensity and allelic imbalance and as such display the varying allele counts and copy numbers. Longer/larger segments have bigger circles. The varying coloration of the segments correspond to the amount of segments, since greater color scale variation is needed for a greater number of segments, and where they are located on the chromosome. They coincide and should be compared with the middle plot. Darker grey circles show more content as they are ontop of eachother.

MIDDLE
Vertical axis: Total Intensity
Horizontal axis: Chromosomal coordinate

The chromosome in questions total intensity plotted against the position on the chromosome.

BOTTOM
Vertical axis: Allelic Imbalance
Horizontal axis: Chromosomal coordinate

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

Author(s)

Markus Mayrhofer, markus.mayrhofer@medsci.uu.se
Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se

See Also

patchwork.CG.plot
CG_karyotype