lineup (version 0.44)

plot.lineupdist: Plot summary of inter-individual distances

Description

Plot histograms of self-self and self-nonself distances from a distance matrix calculated by distee() or disteg().

Usage

# S3 method for lineupdist
plot(x, breaks = NULL, add.rug = TRUE, what = c("both", "ss", "sn"), ...)

Value

None.

Arguments

x

Output of distee() or disteg().

breaks

Optional vector of breaks, passed to graphics::hist(), though if it is length 1, we interpret it as the number of breaks and ensure that both histograms use the same set of breaks.

add.rug

If true, also include graphics::rug() below histograms.

what

Indicates whether to plot both self-self and self-nonself distances (or correlations) or just one or the other. ("ss" indicates self-self and "sn" indicates self-nonself.)

...

Ignored at this point.

Author

Karl W Broman,

Details

We call pulldiag() and omitdiag() to get the self-self and self-nonself distances.

If all of the self-self distances are missing, we plot just the self-nonself distances.

See Also

pulldiag(), distee(), plot2dist()

Examples

data(expr1, expr2)

expr1 <- expr1[,1:500]
expr2 <- expr2[,1:500]

# distance as correlation
d <- distee(expr1, expr2, "cor")

# plot histograms of self-self and self-nonself correlations
plot(d)