tntplot3: detailed plot with 2 data tracks

In vjcitn/tnt4dn8: TnT applications with GWAS in dn8 format

detailed plot with 2 data tracks

Description

detailed plot with 2 data tracks

Usage

tntplot3(
  tab,
  tab2,
  snpcolor = "lightblue",
  genecolor = "darkgreen",
  txcolor = "darkred",
  GT = NULL,
  tt = NULL,
  maxp = 0.1,
  trunc_mlp = 90,
  lab1 = "track1",
  lab2 = "track2"
)

Arguments

tab	data.frame, main GWAS
tab2	data.frame, second set of locations and scores
snpcolor	character(1)
genecolor	character(1)
txcolor	character(1)
GT	defaults to NULL, otherwise a GeneTrackFromTxDb-like object from TnT
tt	defaults to NULL, otherwise a TxTrackFromTxDb-like object from TnT
maxp	numeric(1) if non-NULL loci with p-values greater than this are excluded
trunc_mlp	numeric(1) defaults to 300, -log10p greater than this are reset to this value
lab1	character(1) label for first scored track
lab2	character(1) label for second scored track

Examples

if (requireNamespace("TnT") & requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene")) {
data(gtex_b38_lung_chr20_exc)
data(limgwcat_b38)
cands = avail_syms_gtex()
cands
chk2 = gtex_b38_lung_chr20_exc |> filter_sym(cands[3], radius=5e4) |> as.data.frame()
chk3 = limgwcat_b38 |> filter_sym(cands[3], radius=5e4) |> as.data.frame()
print(tntplot3(chk2, chk3, lab1="GTEx Lung", lab2="EBI GWAS cat"))
}

vjcitn/tnt4dn8 documentation built on Sept. 10, 2022, 11:17 a.m.