qtl2: plot_genes – R documentation

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plot_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

plot_genes(
  genes,
  minrow = 4,
  padding = 0.2,
  colors = c("black", "red3", "green4", "blue3", "orange"),
  scale_pos = 1,
  start_field = "start",
  stop_field = "stop",
  strand_field = "strand",
  name_field = "Name",
  ...
)

Arguments

`genes`	Data frame containing `start` and `stop` in Mbp, `strand` (as `"-"`, `"+"`, or `NA`), and `Name`.
`minrow`	Minimum number of rows of genes in the plot
`padding`	Proportion to pad with white space around the genes
`colors`	Vectors of colors, used sequentially and then re-used.
`scale_pos`	Factor by which to scale position (for example, to convert basepairs to Mbp)
`start_field`	Character string with name of column containing the genes' start positions.
`stop_field`	Character string with name of column containing the genes' stop positions.
`strand_field`	Character string with name of column containing the genes' strands.
`name_field`	Character string with name of column containing the genes' names.
`...`	Optional arguments passed to `plot()`.

Value

None.

Hidden graphics parameters

Graphics parameters can be passed via .... For example, xlim to control the x-axis limits. These are not included as formal

Examples

genes <- data.frame(chr = c("6", "6", "6", "6", "6", "6", "6", "6"),
                    start = c(139988753, 140680185, 141708118, 142234227, 142587862,
                              143232344, 144398099, 144993835),
                    stop  = c(140041457, 140826797, 141773810, 142322981, 142702315,
                              143260627, 144399821, 145076184),
                    strand = c("-", "+", "-", "-", "-", NA, "+", "-"),
                    Name = c("Plcz1", "Gm30215", "Gm5724", "Slco1a5", "Abcc9",
                             "4930407I02Rik", "Gm31777", "Bcat1"),
                    stringsAsFactors=FALSE)

# use scale_pos=1e-6 because data in bp but we want the plot in Mbp
plot_genes(genes, xlim=c(140, 146), scale_pos=1e-6)

qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16