plotColorbar: Colorbar

In dcifer: Genetic Relatedness Between Polyclonal Infections

Colorbar

Description

Creates a colorbar for a plot.

Usage

plotColorbar(
  rlim = c(0, 1),
  by = 0.1,
  at = NULL,
  horiz = FALSE,
  col = grDevices::hcl.colors(301, "YlGnBu", rev = TRUE),
  ...
)

Arguments

rlim	the range of values to be represented by colors.
by	increment size for tickmark locations. Ignored if at is provided.
at	a vector of tickmark locations.
horiz	a logical value specifying if the colorbar should be drawn horizontally.
col	the colors for the colorbar.
...	other graphical parameters.

Details

The colorbar will fill the whole plotting region, which needs to be specified outside of this function to control proportions and location of the colorbar (see examples). To match the colors in the main plot, rlim values should be the same for plotRel and plotColorbar; if rlim = NULL or rlim = NA in plotRel, provide the actual range of relatedness estimates for plotColorbar (see examples).

Value

NULL; called for plotting.

See Also

plotRel for plotting relatedness estimates.

Examples

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

# colorbar on the side of the main plot
layout(matrix(1:2, 1), width = c(7, 1))
par(mar = c(2, 0, 2, 0) + 0.1)
# make symmetric matrix
dmat <- dres[, , "estimate"]
dmat[upper.tri(dmat)] <- t(dmat)[upper.tri(t(dmat))]
isig <- which(dres[, , "p_value"] <= 0.05, arr.ind = TRUE)
plotRel(dmat, draw_diag = TRUE, isig = rbind(isig, isig[, 2:1]))
abline(v = 26, h = 26, col = "gray45", lty = 5)
par(mar = c(2, 1, 2, 2) + 0.1)
plotColorbar()

# shorter colorbar, tick mark locations provided
par(mar = c(2, 0, 2, 0) + 0.1)
plotRel(dmat, draw_diag = TRUE, isig = rbind(isig, isig[, 2:1]))
par(mar = c(5, 0.5, 5, 2.5) + 0.1)
plotColorbar(at = c(0.0625, 0.125, 0.25, 0.5, 0.78))
par(parstart)

# triangular matrix, inset horizontal colorbar
par(mar = c(1, 1, 1, 1))
plotRel(dres, rlim = NULL, draw_diag = TRUE, border_diag = 1, alpha = 0.05)
par(fig = c(0.3, 1.0, 0.73, 0.83), new = TRUE)
rlim <- range(dres[, , 1], na.rm = TRUE)
plotColorbar(rlim = rlim, at = c(0.2, 0.4, 0.6, 0.8), horiz = TRUE)
par(parstart)

dcifer documentation built on May 29, 2024, 9 a.m.