plot.geneJAM: Plot diagnostics for an geneJAM object

In abuchardt/EdGwas: Joint regression Analysis of Multiple traits based on GENEtic relationships

Plot diagnostics for an geneJAM object

Description

Two plots (selectable by which) are currently available: a plot of the mean standard error curve produced by geneJAM i.e., the MSE and upper and lower standard deviation curves plotted against the values of rho used in the fits, and an adjacency matrix plot for rho.min.

Usage

## S3 method for class 'geneJAM'
plot(
  x,
  which = c(1L:2L),
  main = "",
  xlab = NULL,
  ylab = NULL,
  ask = prod(par("mfcol")) < length(which) && dev.interactive(),
  pointsCol = "#D95F02",
  ylim = NULL,
  xlim = NULL,
  col = NULL,
  ...
)

Arguments

x	Fitted "geneJAM" object.
which	If a subset of the plots is required, specify a subset of the numbers 1:5.
main	An overall title for the plot: see title
xlab	A title for the x axis: see title
ylab	A title for the y axis: see title
ask	Logical; if TRUE, the user is asked before each plot, see par(ask=.).
pointsCol	The color for points corresponding to rho.min and rho.1se. Default is pointsCol = "#D95F02".
ylim	The y limits of the plot.
xlim	The x limits of the plot.
col	The color to be used for the curve. Default is col = "grey40".
...	Other paramters to be passed through to plotting functions.

Details

Plots are produced, and nothing is returned.

See Also

geneJAM

Examples

N <- 500
q <- 10
set.seed(1)
x <- matrix(sample(0:2, N*q, replace=TRUE), nrow=N, ncol=q)
B <- matrix(0, nrow = q, ncol = q)
B[1, 1:2] <- 10
y <- x %*% B + matrix(rnorm(N*q), nrow = N, ncol = q)
###
pc <- geneJAM(x, y)
plot(pc, 1)
plot(pc, 2)

abuchardt/EdGwas documentation built on Nov. 28, 2022, 11:49 a.m.