qtl2ggplot (version 1.2.6)

ggplot_genes: Plot gene locations for a genomic interval

Description

Plot gene locations for a genomic interval, as rectangles with gene symbol (and arrow indicating strand/direction) below.

Usage

ggplot_genes(
  object,
  xlim = NULL,
  minrow = 4,
  padding = 0.2,
  colors = c("black", "red3", "green4", "blue3", "orange"),
  ...
)
# S3 method for genes
autoplot(object, ...)

Value

None.

Arguments

object

Object of class object

xlim

x-axis limits (in Mbp)

minrow

Minimum number of rows of object

padding

Proportion to pad with white space around the object

colors

Vectors of colors, used sequentially and then re-used.

...

Optional arguments passed to plot.

Examples

filename <- file.path("https://raw.githubusercontent.com/rqtl",
                      "qtl2data/master/DOex", 
                      "c2_genes.rds")
tmpfile <- tempfile()
download.file(filename, tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

ggplot_genes(gene_tbl)