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)
# A qtlClaaifier/qtl2dplot coupling example:
ucsc_modified <- bind_rows(ucsc,APOC,AMY,C4B,HIST,HBA)
pqtls <- select(merged,prot,SNP,log.P.) %>%
         mutate(log10p=-log.P.) %>%
         left_join(caprion_modified) %>%
         select(Gene,SNP,prot,log10p)
posSNP <- select(merged,SNP,Chr,bp)
cis.vs.trans <- qtlClassifier(pqtls,posSNP,ucsc_modified,1e6) %>%
                mutate(geneChrom=as.integer(geneChrom),
                       cis=if_else(Type=="cis",TRUE,FALSE))
head(cis.vs.trans)
    Gene             SNP  prot log10p geneChrom geneStart  geneEnd SNPChrom    SNPPos  cis
   YWHAB 8:111907280_A_T 1433B   7.38        20  43530174 43535076        8 111907280 FALSE
     A2M 14:34808001_A_T  A2MG   7.51        12   9220421  9268445       14  34808001 FALSE
    APEH  1:12881809_A_G  ACPH   7.83         3  49711834 49720772        1  12881809 FALSE
     PGD 2:121896327_A_G  6PGD   7.79         1  10459174 10479803        2 121896327 FALSE
SERPINF2  17:1618262_C_T  A2AP  12.59        17   1648289  1657825       17   1618262  TRUE
    PGLS 19:54327869_G_T  6PGL   9.87        19  17622481 17631887       19  54327869 FALSE
qtl2dplot(cis.vs.trans,chrlen=gap::hg19,
          snp_name="SNP",snp_chr="SNPChrom",snp_pos="SNPPos",
          gene_chr="geneChrom",gene_start="geneStart",gene_end="geneEnd",
          trait="prot",gene="Gene",
          TSS=TRUE,cis="cis",plot=TRUE,cex.labels=0.6,cex.points=0.6,
          xlab="pQTL position",ylab="Gene position")

## End(Not run)

gap documentation built on Sept. 11, 2024, 5:36 p.m.