plot_scan1_heatmap: Heat map of scan1 results with multiple traits

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Heat map of scan1 results with multiple traits

Description

Heat map of multiple scan1 results

Usage

plot_scan1_heatmap(
  x,
  map,
  chr = NULL,
  y = NULL,
  gap = NULL,
  zlim = NULL,
  color_scheme = c("viridis", "gray", "revgray", "heat", "terrain", "topo", "rainbow"),
  col = NULL,
  n_colors = 256,
  swap_axes = FALSE,
  chrlines = NULL,
  rescale_by = c("none", "col", "chr", "both"),
  ...
)

Arguments

x	An object of class "scan1", as output by scan1().
map	A list of vectors of marker positions, as produced by insert_pseudomarkers().
chr	Selected chromosomes to plot; a vector of character strings.
y	Vector with length equal to ncol(x), defining the y-axis scale of the heat map. (If the multiple LOD scores are for a quantitative variable like time, these are the corresponding times.)
gap	Gap between chromosomes. The default is 1% of the total genome length.
zlim	Z-axis limits (a pair of numbers)
color_scheme	Color scheme for the heatmap (ignored if col is provided).
col	Optional vector of colors for the heatmap.
n_colors	Number of z-axis colors (ignored if col is provided).
swap_axes	If TRUE, put chromosome position on y-axis and lod columns on x-axis (default is to have chromosome position on x-axis and lod columns on y-axis)
chrlines	Color of lines at chromosome breaks (NULL for default choices; NA to skip them).
rescale_by	Rescale the LOD scores by column, chromosome, or both, by subtracting the maximum value. The default is not to rescale.
...	Additional graphics paramaters.

Value

None.

See Also

plot_scan1(), plot_lodpeaks(), graphics::image(); plot_colorscale()

Examples

grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map, error_prob=0.002)
out <- scan1(probs, grav2$pheno)
plot_scan1_heatmap(out, map)

# make the y-axis quantitative
y <- grav2$phenocovar$time
plot_scan1_heatmap(out, map, y=y, ylab=colnames(grav2$phenocovar))

# plot with colors white -> darkslateblue, and with color scale
col <- colorRampPalette(c("white", "darkslateblue"))(256)
zlim <- c(0, maxlod(out))
layout(cbind(1,2), width=c(3,1))
plot_scan1_heatmap(out, map, y=y, ylab=colnames(grav2$phenocovar),
                   col=col, zlim=zlim)
plot_colorscale(col=col, zlim=zlim)

qtl2 documentation built on July 6, 2026, 5:11 p.m.