View source: R/allele.plotter.R
allele.plotter.whole | R Documentation |
This function takes a genome scan object from scan.h2lmm() and plots out allele effect estimates based on regression coefficients or BLUPs.
allele.plotter.whole( scan.object, just.these.chr = NULL, scale = "Mb", imp.confint.alpha = NULL, main.colors = c(rgb(240, 240, 0, maxColorValue = 255), rgb(128, 128, 128, maxColorValue = 255), rgb(240, 128, 128, maxColorValue = 255), rgb(16, 16, 240, maxColorValue = 255), rgb(0, 160, 240, maxColorValue = 255), rgb(0, 160, 0, maxColorValue = 255), rgb(240, 0, 0, maxColorValue = 255), rgb(144, 0, 224, maxColorValue = 255)), use.legend = TRUE, main = "", my.bty = "n", my.lwd = 1.25, set.plot.limit = c(-10, 10), my.legend.cex = 0.6, my.legend.pos = "topright", transparency = 0.6, y.max.manual = NULL, y.min.manual = NULL, my.y.line = 2, my.y.axis.cex = 1, my.y.lab.cex = 0.7, my.x.lab.cex = 0.7, no.title = FALSE, override.title = NULL, add.chr.to.label = FALSE, alternative.labels = NULL, axis.cram = TRUE, include.x.axis.line = TRUE )
scan.object |
A scan.h2lmm() object that had return.allele.effects=TRUE. |
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: CC founder colors. The colors that correspond to the founder alleles. |
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.lwd |
DEFAULT: rep(1.5, 8). Specifies the lwds for the alleles. |
my.legend.cex |
DEFAULT: 0.6. Specifies the size of the text in the legend. |
my.legend.pos |
DEFAULT: "topright". Specifies where to put the legend, if specified in use.legend. |
transparency |
DEFAULT: 0.6. The transparency level for the confidence bands. 0 is invisible, 1 is solid. |
y.max.manual |
DEFAULT: NULL. Manually adds a max y-value. |
y.min.manual |
DEFAULT: NULL. Manually adds a min y-value. |
no.title |
DEFAULT: FALSE. If TRUE, produces a plot with no title, not even the automatic title components like formula and sample size. |
override.title |
DEFAULT: NULL. If non-null, overrides automatic title components like formula and sample size. |
add.chr.to.label |
DEFAULT: FALSE. If TRUE, "chr" precedes integers on the x-axis. |
alternative.labels |
DEFAULT: NULL. If non-null, specifies alternative labels for the founder alleles. |
axis.cram |
DEFAULT: TRUE. This makes the plot much more likely to include all chromosome labels. With small plots, this could lead to overlapping labels. |
include.x.axis.line |
DEFAULT: TRUE. IF TRUE, this option adds an x-axis line with ticks between chromosomes. |
allele.plotter.whole()
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