plot_genes: Plot gene locations for a genomic interval

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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. (The values of the corresponding field can be character strings "+" or "-", or numeric +1 or -1.)
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)

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.