Description Usage Arguments Details Author(s) See Also
A general overview of the whole genome of the sample.
1 |
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. |
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.
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
patchwork.plot
karyotype_chroms
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