Description Usage Arguments References See Also
View source: R/plotQTLScanone.R
Plotting function based on R/qtl plot.scanone
(Broman
et al. 2003) and qqman manhattan
(Turner 2014).
Plots a scanone
result as a LOD curve (with type
set
to 'l'
) or as a Manhattan plot (with type
set to
'p'
). If no plot type is specified, this is set automatically
based on marker density.
1 2 3 |
x |
An R/qtl |
chr |
Vector indicating which sequences to plot. If no sequences are specified, all are plotted. |
lodcolumn |
In a |
qtl.intervals |
A |
threshold |
A single |
col |
Analogous to the standard |
gap |
Gap (in cM) between chromosomes in multi-chromosome plots. |
phenotype |
Name of the phenotype, to be shown in plot information. |
type |
Type of plot. Set to |
... |
Unused arguments. |
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)
Turner SD (2014) qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. (bioRXiv)
Other plot functions: plotQTLScantwo
Other QTL functions: estPhysicalPositions
,
getQTLFeatures
,
getQTLIntervals
, getQTLPeaks
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