Description Usage Arguments Examples
This function takes the genome scan output from scan.h2lmm() and flexibly plots out the genome scan.
1 2 3 4 5 6 | 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. |
1 |
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