qtl2dplot: 2D QTL plot

In gap: Genetic Analysis Package

2D QTL plot

Description

2D QTL plot

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"
)

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.

Details

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

Value

positional information.

Examples

## Not run: 
INF <- Sys.getenv("INF")
d <- read.csv(file.path(INF,"work","INF1.merge.cis.vs.trans"),as.is=TRUE)
r <- qtl2dplot(d)

## End(Not run)

gap documentation built on Aug. 26, 2023, 5:07 p.m.