plot_genes: Plot gene locations for a genomic interval

In rqtl/qtl2plot: Data Visualization for QTL Experiments

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 graphics::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)
plot_genes(genes, xlim=c(140, 146))

rqtl/qtl2plot documentation built on May 28, 2019, 2:36 a.m.