plot_locus.effect.from.scan: Plot the regression coefficients as allele effects for a...
In gkeele/miqtl: Suite of QTL Mapping Functions

plot_locus.effect.from.scan

R Documentation

Plot the regression coefficients as allele effects for a single locus as a caterpillar plot from a scan object

Description

This function takes a scan object from scan.h2lmm() and plots out allele effect estimates based on regression coefficients for a single locus. If multiple imputation was used, these correspond to confidence intervals on the mean effect over imputations.

Usage

plot_locus.effect.from.scan(
  scan.object,
  locus,
  main = "",
  names = c("ACI", "BN", "BUF", "F344", "M520", "MR", "WKY", "WN"),
  col = 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)),
  add.connect.line = TRUE,
  connect.lwd = 2,
  connect.lty = 1,
  connect.col = "black",
  add = FALSE,
  ...
)

Arguments

`scan.object`	A scan object from scan.h2lmm(). Can work for ROP or multiple imputation.
`locus`	The locus for which effect estimates are need. The locus must be included in the scan.
`main`	DEFAULT: "". The title to included in the plot.
`names`	DEFAULT: c("ACI", "BN", "BUF", "F344", "M520", "MR", "WKY", "WN"). These are the strains used in the HS rats.
`col`	DEFAULT: 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)). These are the established Collaborative Cross colors.
`add.connect.line`	DEFAULT: TRUE. Adds a connection line between the effects (or their mean).
`connect.lwd`	DEFAULT: 2. The line width of the connection line, if it is included
`connect.col`	DEFAULT: "black". The color of the connection line, if it is included
`add`	DEFAULT: FALSE. If TRUE, a new plot is not initiated. The purpose is to allow multiple sets of effects to be included on a single plot.
`connect.ltt`	DEFAULT: 1. The line type of the connection line, if it is included