snp.genome.plotter.w.r2: Plot a single chromosome window of a SNP-based genome scan...
In gkeele/kqtl: Suite of QTL Mapping Functions

Description Usage Arguments Examples

This function takes the outputs from imputed.snp.scan.h2lmm() and pairwise.cor.snp.scan() and plots the SNP association for a single chromosome, overlayed with r^2 information for a specified SNP.

snp.genome.plotter.w.r2(snp.scan, r2.object, scale = "Mb",
  y.max.manual = NULL, title = "", alt.col = NULL, this.cex = 1,
  hard.thresholds = NULL, thresholds.col = "red",
  thresholds.legend = NULL, my.legend.cex = 0.6,
  my.legend.pos = "topleft", r2.bounds = NULL)

`snp.scan`	An imputed.snp.scan.h2lmm() object.
`r2.object`	A pairwise.cor.snp.scan() object.
`scale`	DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM are expected.
`y.max.manual`	DEFAULT: NULL. Manually adds a max y-value. Allows multiple genome scans to easily be on the same scale.
`title`	DEFAULT: "". Manually adds a max ylim to the plot. Allows multiple genome scans to easily be on the same scale.
`alt.col`	DEFAULT: NULL. Allows for a custom color vector for individual SNPs.
`this.cex`	DEFAULT: 1. Allows for the adjustment of the cex value for the main plot.
`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,
`my.legend.cex`	DEFAULT: 0.6. Specifies the size of the text in the legend.
`my.legend.pos`	DEFAULT: "topright". Specified position of the legend on the plot.
`r2.bounds`	DEFAULT: NULL. If NULL, no interval is depicted on the plot. If set to a value in [0,1], will include interval based on the given r2 on the plot.