genome.plotter.whole: Plot one or more haplotype-based genome scans flexibly (whole...
In gkeele/kqtl: Suite of QTL Mapping Functions

This function takes the genome scan output from scan.h2lmm() and flexibly plots out the genome scan.

genome.plotter.whole(scan.list, use.lod = FALSE, just.these.chr = NULL,
  scale = "Mb", main.colors = c("black", "gray48", "blue"),
  use.legend = TRUE, main = "", my.legend.cex = 0.6,
  my.legend.lwd = NULL, my.legend.pos = "topright", y.max.manual = NULL,
  hard.thresholds = NULL, thresholds.col = "red",
  thresholds.legend = NULL)

`scan.list`	A list of scan.h2lmm() objects that are to be plotted within the same genome scan plot.
`use.lod`	DEFAULT: FALSE. Plots either the LOD score or the -log10 p-value.
`just.these.chr`	DEFAULT: NULL. Specifies a subset of the chromosomes to be plotted. NULL results in all chromosomes being plotted.
`scale`	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM are expected.
`main.colors`	DEFAULT: "black". The color of the main association score to be plotted.
`use.legend`	DEFAULT: TRUE. Include a legend for the different associations. If TRUE, the labels are the names of the non.mi.scan.list object.
`main`	DEFAULT: NULL. Adds a title above the model.
`my.legend.cex`	DEFAULT: 0.6. Specifies the size of the text in the legend.
`my.legend.lwd`	DEFAULT: NULL. If NULL, all lines have lwd=1.5. If not, option specifies the lwds.
`my.legend.pos`	DEFAULT: "topright". Specifies where to put the legend, if specified in use.legend.
`y.max.manual`	DEFAULT: NULL. Manually adds a max y-value. Allows multiple genome scans to easily be on the same scale.
`hard.thresholds`	DEFAULT: NULL. Specify one or more horizontal threshold lines.
`thresholds.col`	DEFAULT: "red". Set the colors of the specified thresholds.
`thresholds.legend`	DEFAULT: NULL. If non-NULL, string arguments used as labels in thresholds legend. If NULL, no threshols legend is used.