shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments References See Also

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.

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plotQTLScanone(x, chr = NULL, lodcolumn = NULL, qtl.intervals = NULL,
  threshold = NULL, col = c("gray10", "gray60"), gap = 25,
  phenotype = NULL, type = NULL, ...)

`x`	An R/qtl `scanone` object.
`chr`	Vector indicating which sequences to plot. If no sequences are specified, all are plotted.
`lodcolumn`	In a `scanone` or equivalent object, this parameter indicates which LOD column to consider. In other objects with LOD-column-associated elements, this parameter indicates which LOD-column-associated element to consider. This must be either a LOD column name or an index with respect to the set of LOD columns. If no LOD column is specified and one such column is found, that column is used by default; otherwise a LOD column must be specified.
`qtl.intervals`	A `qtlintervals` object created from the same data as the `scanone` object. These intervals are added to the plot, unless the median interval size is too small to be distinguishable. Threshold information is taken from this object, if available.
`threshold`	A single `numeric` LOD significance threshold, or an object (e.g. `summary.scanoneperm`) containing one such threshold and its associated significance level.
`col`	Analogous to the standard `'col'` plotting parameter. This is recycled to match the number of sequences being plotted. As in the package qqman, this defaults to two alternating monochrome shades.
`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 `'l'` to output a stanard LOD curve, or to `'p'` for a Manhattan plot of individual LOD scores.
`...`	Unused arguments.