genome.plotter.whole: Plot one or more haplotype-based genome scans flexibly (whole...

In gkeele/miqtl: Suite of QTL Mapping Functions

Plot one or more haplotype-based genome scans flexibly (whole genomes or subset of chromosomes)

Description

This function takes the genome scan output from scan.h2lmm() and flexibly plots out the genome scan.

Usage

genome.plotter.whole(
  scan.list,
  use.lod = FALSE,
  just.these.chr = NULL,
  scale = "Mb",
  main.colors = c("black", "cyan", "darkgreen"),
  distinguish.chr.type = c("color", "box"),
  distinguish.box.col = "gray88",
  distinguish.chr.col = c("gray60", "#008080", "greenyellow"),
  override.col = NULL,
  use.legend = TRUE,
  main = "",
  my.legend.cex = 0.6,
  my.legend.lwd = NULL,
  my.legend.lty = 1,
  my.legend.pos = "topright",
  my.legend.bty = "n",
  y.max.manual = NULL,
  my.y.line = 2,
  my.y.axis.cex = 1,
  my.y.lab.cex = 0.7,
  my.x.lab.cex = 0.7,
  my.x.labels = TRUE,
  my.x.lab.padj = -1.5,
  no.title = FALSE,
  override.title = NULL,
  my.title.line = NA,
  title.cex = 1,
  hard.thresholds = NULL,
  thresholds.col = "red",
  thresholds.legend = NULL,
  thresholds.lwd = NULL,
  thresholds.legend.pos = "topleft",
  thresholds.lty = NULL,
  add.chr.to.label = FALSE,
  axis.cram = TRUE,
  include.x.axis.line = TRUE,
  mark.locus = NULL,
  mark.locus.col = "red",
  which.mark = 1,
  mark.lwd = 4,
  mark.manual = list(chr = NULL, pos = NULL),
  add.polygon = FALSE,
  which.polygon = 1,
  my.type = "l",
  my.pch = 20,
  my.cex = 0.5,
  use_bold_axis = FALSE,
  axis_lwd = 1,
  include_y_axis = TRUE
)

Arguments

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.
distinguish.chr.type	DEFAULT: "color". The default specifies rectangular block backgrounds to distinguish adjacent chromosomes. The "color" option specifies alternating colors.
distinguish.box.col	DEFAULT: "gray88". If distinguish.chr.type="box" is specified, this argument provides the color of the background rectangle.
distinguish.chr.col	DEFAULT: "gray60". If distinguish.chr.type="color" is specified, this argument provides the alternating color. Multiple colors should be specified if multiple scans are included in the plot.
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.
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.
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.
add.chr.to.label	DEFAULT: FALSE. If TRUE, adds "Chr" before every chromosome label. If FALSE, "Chr" is added as an axis label under the y-axis.
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.

Examples

genome.plotter.whole()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.