View source: R/genome_plotter.R
genome.plotter.chr | R Documentation |
This function takes the genome scan output from scan.h2lmm() and plots the portion that corresponds to a single chromosome. When multiple imputations are used, includes the 95% confidence band on the median.
genome.plotter.chr(
scan.object,
chr,
use.lod = FALSE,
scale = c("Mb", "cM"),
main.col = "black",
median.band.col = "gray88",
main = "",
no.title = FALSE,
override.title = NULL,
my.y.line = 2,
my.y.axis.cex = 1,
y.max.manual = NULL,
make.y.axis.sparse = FALSE,
my.ylab.cex = 1,
my.x.line = 3,
my.x.axis.cex = 1,
my.xlab.cex = 1,
x.padj = 1,
my.x.axis.at = NULL,
my.x.labels = TRUE,
override.xlab = NULL,
my.title.line = 0.5,
title.cex = 1,
my.lwd = 1.5,
override.ylab = NULL,
my.legend.cex = 0.6,
my.type = "l",
point.cex = 0.5,
hard.thresholds = NULL,
thresholds.col = "red",
thresholds.legend = NULL,
include.qtl.rug = FALSE,
rug.pos = NULL,
rug.col = "gray50",
physical.dist.is.Mb = TRUE,
use.frame.plot = FALSE
)
scan.object |
A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted. |
chr |
The chromosome to be plotted. |
use.lod |
DEFAULT: FALSE. Plots either the LOD score or the -log10 p-value. |
scale |
DEFAULT: "Mb". Specifies the scale of genomic position to be plotted. Either Mb or cM can be used. |
main.col |
DEFAULT: "black". The color of the main association score to be plotted. |
median.band.col |
DEFAULT: "gray88". The color of the 95% confident band plotted around the median. |
main |
DEFAULT: "". Adds a title above the model. |
no.title |
DEFAULT: FALSE. If TRUE, no title is printed. |
override.title |
DEFAULT: NULL. If a string is specified, it is included on plot without any of the default automated title. |
y.max.manual |
DEFAULT: NULL. Manually adds a max y-value. Allows multiple genome scans to easily be on the same scale. |
my.legend.cex |
DEFAULT: 0.6. Specifies the size of the text in the legend. |
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. |
genome.plotter.chr()
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