plotManhattan: LocusExplorer - Manhattan plot
In oncogenetics/oncofunco: Custom function for Oncogenetics team

plotManhattan

R Documentation

LocusExplorer - Manhattan plot

Description

Manhattan plot for LocusExplorer.

Usage

plotManhattan(
  assoc = NULL,
  LD = NULL,
  geneticMap = NULL,
  suggestiveLine = 5,
  genomewideLine = 8,
  xStart = NULL,
  xEnd = NULL,
  hits = NULL,
  hitsName = hits,
  hitsLabel = TRUE,
  hitsColour = NULL,
  pad = TRUE,
  postprob = FALSE,
  yRangeBy = NULL,
  title = NULL,
  opts = c("Recombination", "LD", "LDSmooth", "SuggestiveLine", "GenomewideLine",
    "Hits")
)

Arguments

`assoc`	SNP association results, data.frame object with c("SNP","BP","P") columns. Required.
`LD`	plink LD output format, data.frame object with c("BP_A","SNP_A","BP_B","SNP_B","R2") columns. Optional/recommended.
`geneticMap`	Recombination map, data.frame object with c("BP", "RECOMB") columns. Subset of one of genetic_map_*_combined_b37.txt, at http://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3/ . Optional.
`suggestiveLine`	Suggestive line, default is 5.
`genomewideLine`	Genomewide link, dafault is 8.
`xStart, xEnd`	Region range, zoom, minimum BP and maximum BP, advised to keep this less than 5Mb.
`hits`	SNP names to label in the plot. Must be present in assoc data.frame.
`hitsName`	alternative SNP names to label in the plot. Default same as 'hits'
`hitsLabel`	Default is TRUE, set to FALSE not to show SNP names on the plot.
`hitsColour`	Default NULL, uses ggplot colours.
`pad`	Default is TRUE, to align plots pad strings with spaces, using oncofunco::strPadLeft().
`postprob`	Default is FALSE, used for LocusExplorer to plot JAM PostProbs instead of Pvalues.
`yRangeBy`	y-axis ticks, setting to 5 means ticks will be placed at 'c(0, 5, 10, ...)'.
`title`	character string for plot title. Default is NULL, i.e.: no plot title.
`opts`	Default is c("Recombination","LD","LDSmooth","SuggestiveLine","GenomewideLine","Hits"), parts of plot to display.