snp.genome.plotter.w.r2 | R Documentation |
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", zoom.in = FALSE, zoom.in.by = 0.1, y.max.manual = NULL, my.y.line = 2, my.y.axis.cex = 1, my.ylab.cex = 1, title = "", override.title = NULL, my.title.line = NA, title.cex = 1, alt.col = NULL, this.cex = 1, hard.thresholds = NULL, thresholds.col = "red", thresholds.legend = NULL, my.legend.cex = 0.6, my.legend.pos = "topleft", thresholds.lty = 2, thresholds.lwd = 1, my.bty = "n", r2.bounds = NULL, bounds.col = "gray", high.color = "red", low.color = "blue", add.outline = FALSE, include.ramp = TRUE, ramp.cex = 0.7 )
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. |
snp.genome.plotter.w.r2()
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