View source: R/genome_plotter.R
genome.plotter.to.pdf | R Documentation |
This function takes the genome scan output from scan.h2lmm() and plots the whole genome and single chromosome zoom-ins for all the specified chromosomes. When multiple imputations are used, includes the 95% confidence band on the median in the zoomed-in plots.
genome.plotter.to.pdf(
scan.object,
chr = c(1:19, "X"),
use.lod = FALSE,
scale = c("Mb", "cM"),
main.col = "black",
median.band.col = "gray88",
main = "",
no.title = FALSE,
override.title = NULL,
y.max.manual = NULL,
hard.thresholds = NULL,
thresholds.col = "red",
thresholds.legend = NULL,
pdf.output.path,
pdf.height = 5,
pdf.width = 9,
...
)
scan.object |
A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted. |
chr |
DEFAULT: c(1:19, "X"). The chromosomes to be plotted. DEFAULT is all the mouse chromosomes. |
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 are expected. |
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. |
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 thresholds legend is used. |
pdf.output.path |
That path of the PDF file to be generated. |
pdf.height |
DEFAULT: 5. The height of an individual pages of the PDF. |
pdf.width |
DEFAULT: 9. The width of an individual pages of the PDF. |
main.colors |
DEFAULT: "black". The color of the main association score to be plotted. |
genome.plotter.to.pdf()
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