2D QTL plot
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"
)positional information.
Data to be used.
lengths of chromosomes for specific build: hg18, hg19, hg38.
variant name.
variant chromosome.
variant position.
gene chromosome.
gene start position.
gene end position.
trait name.
gene name.
to use TSS when TRUE.
cis variant when TRUE.
A specific value to show.
to plot when TRUE.
Axis label extension factor.
Data point extension factor.
X-axis title.
Y-axis title.
This function is both used as its own for a 2d plot and/or generate data for a plotly counterpart.