panel.geneplot: Plot genes along a linear axis

In m-jahn/lattice-tools: Panel functions and wrappers that extend the R lattice universe

Plot genes along a linear axis

Description

This panel function allows to draw genes with start and end coordinates as main input. Optional vectors for 'gene_name' or 'gene_strand' must have same length as 'x', 'y'. This function supports paneling and grouping (e.g. by gene functional category) just as regular panel functions.

Usage

panel.geneplot(
  x,
  y,
  groups = NULL,
  subscripts = NULL,
  gene_name = NULL,
  gene_strand = NULL,
  draw_labels = TRUE,
  arrows = TRUE,
  origin = 0,
  height = 1,
  offset = 0,
  tip = NULL,
  col = NULL,
  col_labels = grey(0.3),
  rot_labels = 35,
  dist_labels = 1.5,
  group.number = NULL,
  ...
)

Arguments

x, y	(numeric) start and end positions e.g. in bp, respectively
groups	grouping variable passed down from xyplot (does not need to be specified)
subscripts	subscripts passed down from xyplot (does not need to be specified)
gene_name	(character) optional names of the genes to be plotted.
gene_strand	(character) optional strand information for each gene ('+' or '-').
draw_labels	(logical) if gene name labels are drawn
arrows	(logical) draw arrow like boxes (default) or plain or boxes
origin	(numeric) the horizontal line that serves as origin for drawing genes
height	(numeric) height of the boxes/arrows
offset	(numeric) distance of boxes/arrows from origin (default: 0)
tip	(numeric) pointedness of the arrow head (in native X units. Defaults to a 30th of x scale)
col	(character) color (vector) to be used for boxes/arrows. The default, NULL, uses colors supplied by the top level function.
col_labels	(character) color used for text labels and lines
rot_labels	(numeric) degree of rotation for text labels (0 for no rotation at all)
dist_labels	(numeric) relative distance of labels to origin, defaults to 1.5 times box height
group.number	internal parameter only used when function is called as panel.groups argument from within panel.superpose. Does not need to be specified manually.
...	other arguments passed to the function

Examples

library(lattice)

# table with dummdy genetic loci
genes <- data.frame(
  gene_name = c("abc", "def", "ghi", "jkl"),
  gene_strand = c("+", "+", "+", "-"),
  gene_start = c(123, 178, 245, 310),
  gene_end = c(167, 233, 297, 354)
)

# plot genes on a linear map
xyplot(gene_end ~ gene_start, genes,
  groups = gene_strand,
  scales = list(y = list(draw = FALSE)),
  xlim = c(80, 380), ylim = c(-3,2),
  xlab = "", ylab = "",
  gene_strand = genes[["gene_strand"]],
  gene_name = genes[["gene_name"]],
  panel = function(x, y, ...) {
    panel.grid(h = -1, v = -1, col = grey(0.9))
    panel.geneplot(x, y, arrows = TRUE, ...)
  }
)

# same example with customized arrows
xyplot(gene_end ~ gene_start, genes,
  groups = gene_strand,
  scales = list(y = list(draw = FALSE)),
  xlim = c(80, 380), ylim = c(-3,2),
  xlab = "", ylab = "",
  gene_strand = genes[["gene_strand"]],
  gene_name = genes[["gene_name"]],
  panel = function(x, y, ...) {
    panel.grid(h = -1, v = -1, col = grey(0.9))
    panel.geneplot(x, y, arrows = TRUE, offset = 0.5, 
      height = 0.6, rot_labels = 0, tip = 3, col_labels = 1, ...)
  }
)

m-jahn/lattice-tools documentation built on Dec. 3, 2023, 11:14 p.m.