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Plot Relatedness Estimates

Source: R/plot.R
plotRel.Rd

Represents a matrix of pairwise relatedness estimates with colors corresponding to the levels of relatedness. Optionally, also outlines results of a hypothesis testing. The plot follows a matrix layout.

Usage

plotRel(
  r,
  rlim = c(0, 1),
  isig = NULL,
  alpha = NULL,
  col = grDevices::hcl.colors(101, "YlGnBu", rev = TRUE),
  draw_diag = FALSE,
  col_diag = "gray",
  border_diag = NA,
  lwd_diag = 0.5,
  border_sig = "orangered2",
  lwd_sig = 1.5,
  xlab = "",
  ylab = "",
  add = FALSE,
  idlab = FALSE,
  side_id = c(1, 2),
  col_id = 1,
  cex_id = 0.5,
  srt_id = NULL,
  ...
)

Arguments

r

a matrix or a 3-dimensional array as returned by ibdDat.

rlim

the range of values for colors. If NULL or NA, will be calculated from r.

isig

a matrix with two columns providing indices of relatedness matrix entries to be outlined ("significant" sample pairs). Takes precedence over alpha.

alpha

significance level for hypothesis testing; determines relatedness matrix entries to be outlined. Ignored if isig is not NULL.

col

the colors for the range of relatedness values.

draw_diag

a logical value specifying if diagonal cells should be distinguished from others by a separate color.

col_diag, border_diag, lwd_diag

the color for the fill, the color for the border, and the line width for the border of diagonal entries. Ignored if draw_diag = FALSE.

border_sig, lwd_sig

the color and the line width for outlining entries specified by isig or alpha.

xlab, ylab

axis labels.

add

a logical value specifying if the graphics should be added to the existing plot (useful for triangular matrices).

idlab

a logical value specifying if sample ID's should be displayed.

side_id

an integer vector specifying plot sides for sample ID labels.

col_id, cex_id

numeric vectors for the color and the size of sample ID labels.

srt_id

a vector of the same length as side_id specifying rotation angles for sample ID labels. If NULL, the labels will be perpendicular to the axes.

...

other graphical parameters.

Value

NULL; called for plotting.

See also

plotColorbar for a colorbar.

Examples

parstart <- par(no.readonly = TRUE)   # save starting graphical parameters

par(mar = c(0.5, 0.5, 0.5, 0.5))
plotRel(dres, alpha = 0.05, draw_diag = TRUE)

# draw log of p-values in the upper triangle
pmat <- matrix(NA, nrow(dres), ncol(dres))
pmat[upper.tri(pmat)] <- t(log(dres[, , "p_value"]))[upper.tri(pmat)]
pmat[pmat == -Inf] <- min(pmat[is.finite(pmat)])
plotRel(pmat, rlim = NULL, draw_diag = TRUE, col = hcl.colors(101, "PuRd"),
        add = TRUE, col_diag = "slategray2", border_diag = 1)


# symmetric matrix, outline significant in upper triangle, display sample ID
par(mar = c(3, 3, 0.5, 0.5))
dmat <- dres[, , "estimate"]
dmat[upper.tri(dmat)] <- t(dmat)[upper.tri(t(dmat))]
isig <- which(dres[, , "p_value"] <= 0.05, arr.ind = TRUE)
col_id <- rep(c("plum4", "lightblue4"), each = 26)
plotRel(dmat, isig = isig[, 2:1], draw_diag = TRUE, idlab = TRUE,
        col_id = col_id)
abline(v = 26, h = 26, col = "gray45", lty = 5)


# rotated sample ID labels on all sides
par(mar = c(3, 3, 3, 3))
plotRel(dmat, isig = rbind(isig, isig[, 2:1]), border_sig = "magenta2",
        draw_diag = TRUE, idlab = TRUE, side_id = 1:4, col_id = col_id,
        srt_id = c(-55, 25, 65, -35))

par(parstart)