lineup (version 0.44)

plot2dist: Plot two sets of inter-individual distances against one another

Description

Plot two sets of inter-individual distances against one another, colored by self and non-self distances.

Usage

plot2dist(
  d1,
  d2,
  hirow = NULL,
  hicol = NULL,
  xlab = NULL,
  ylab = NULL,
  smoothScatter = FALSE,
  colself = "black",
  colnonself = "gray",
  colhirow = "green",
  colhicol = "orange",
  ...
)

Value

None.

Arguments

d1

Output of distee().

d2

Output of distee().

hirow

Names of rows to highlight in green.

hicol

Names of columns to highlight in orange.

xlab

X-axis label (optional)

ylab

Y-axis label (optional)

smoothScatter

If TRUE, plot non-self distances with graphics::smoothScatter(); if FALSE, use base::plot().

colself

Color to use for the self-self points. If NULL, these aren't plotted.

colnonself

Color to use for the non-self points. If NULL, these aren't plotted.

colhirow

Color to use for the hirow points. If NULL, these aren't plotted.

colhicol

Color to use for the hicol points. If NULL, these aren't plotted.

...

Passed to base::plot() and graphics::points().

Author

Karl W Broman,

See Also

pulldiag(), distee(), summary.lineupdist()

Examples

data(expr1, expr2)

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

# distances as RMS difference and correlation
d_rmsd <- distee(expr1, expr2, "rmsd")
d_cor <- distee(expr1, expr2, "cor")

# plot distances against one another
plot2dist(d_rmsd, d_cor)