ggplot_genes: Plot gene locations for a genomic interval

In qtl2ggplot: Data Visualization for QTL Experiments

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 class 'genes'
autoplot(object, ...)

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.

Value

None.

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)

qtl2ggplot documentation built on March 31, 2023, 6:06 p.m.