genome.plotter.to.pdf: Plot whole genome and single chromosome windows of...
In gkeele/kqtl: Suite of QTL Mapping Functions

Description Usage Arguments Examples

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 = "", 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.
`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.
`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.