gap (version 1.5-1)

qtl2dplot: 2D QTL plot

Description

This function is both used as its own for a 2d plot and/or generate data for a plotly counterpart.

Usage

qtl2dplot(
  d,
  chrlen = gap::hg19,
  snp_name = "SNP",
  snp_chr = "Chr",
  snp_pos = "bp",
  gene_chr = "p.chr",
  gene_start = "p.start",
  gene_end = "p.end",
  trait = "p.target.short",
  gene = "p.gene",
  TSS = FALSE,
  cis = "cis",
  value = "log10p",
  plot = TRUE,
  cex.labels = 0.6,
  cex.points = 0.6,
  xlab = "QTL position",
  ylab = "Gene position"
)

Value

positional information.

Arguments

d

Data to be used.

chrlen

lengths of chromosomes for specific build: hg18, hg19, hg38.

snp_name

variant name.

snp_chr

variant chromosome.

snp_pos

variant position.

gene_chr

gene chromosome.

gene_start

gene start position.

gene_end

gene end position.

trait

trait name.

gene

gene name.

TSS

to use TSS when TRUE.

cis

cis variant when TRUE.

value

A specific value to show.

plot

to plot when TRUE.

cex.labels

Axis label extension factor.

cex.points

Data point extension factor.

xlab

X-axis title.

ylab

Y-axis title.

Examples

if (FALSE) {
INF <- Sys.getenv("INF")
d <- read.csv(file.path(INF,"work","INF1.merge.cis.vs.trans"),as.is=TRUE)
r <- qtl2dplot(d)
}