shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments References See Also

This function is a restricted version of R/qtl function plot.scantwo (Broman et al. 2003), plotting the input scantwo result as a heatmap. The set of palettes are the same as in R/qtl plot.scantwo, except for 'viridis' which uses the recently-developed R package of the same name.

plotQTLScantwo(x, chr = NULL, incl.markers = FALSE, lodcolumn = NULL,
  lower = c("full", "add", "cond-int", "cond-add", "int"), upper = c("int",
  "cond-add", "cond-int", "add", "full"), zscale = TRUE,
  palette = c("viridis", "redblue", "cm", "gray", "heat", "terrain", "topo"),
  phenotype = NULL, ...)

`x`	An R/qtl `scantwo` object.
`chr`	Vector indicating which sequences to plot. If none are specified, all are plotted.
`incl.markers`	When `scantwo` has been run with a fixed non-zero step width, this indicates if markers (as distinct from pseudomarkers) should be included in the plot.
`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.
`lower`	The `scantwo` LOD type to output in the lower triangle of the plot.
`upper`	The `scantwo` LOD type to output in the upper triangle of the plot.
`zscale`	Display a z-scale in the right margin of the plot.
`palette`	Palette to use in the plot. This is equivalent to the R/qtl `plot.scantwo` parameter `'col.scheme'`.
`phenotype`	Name of the phenotype, to be shown in plot information.
`...`	Unused arguments.