Generate manhattan plot — manhattan • rvat

Generate a manhattan plot for an rvatResult object.

manhattan(
  object,
  highlight = NULL,
  label = "label",
  threshold = NULL,
  labelThreshold = NULL,
  labelRepel = FALSE,
  labelSize = NULL,
  contigs = c(),
  title = ""
)

Arguments

object: rvatResult object.
highlight: vector of units/VAR_ids that should be highlighted in red
label: Column name of the labels that are used for significant results
threshold: Fwe threshold (bonferroni applied by default).
labelThreshold: P-value threshold to display labels.
labelRepel: Should the text labels repel away from each other and away from the data points? Defaults to FALSE.
labelSize: Size of the label, defaults to the default used in the ggrepel package.
contigs: Update contig lengths from GRCh37 defaults.
title: Optional title.

Examples

library(rvatData)
data(rvbresults)

# generate manhatan plot
man <- manhattan(rvbresults[rvbresults$varSetName == "ModerateImpact" & rvbresults$test == "firth",],
                 label = "unit", 
                 contigs = "GRCh38")

# if many overlapping gene label, try setting `labelRepel = TRUE`
man <- manhattan(rvbresults[rvbresults$varSetName == "ModerateImpact" & rvbresults$test == "firth",],
                 label = "unit", 
                 labelRepel = TRUE,
                 contigs = "GRCh38")

# alter the significane threshold using the `threshold` parameter
man <- manhattan(rvbresults[rvbresults$varSetName == "ModerateImpact" & rvbresults$test == "firth",],
                 label = "unit", 
                 labelRepel = TRUE,
                 threshold = 1e-5,
                 contigs = "GRCh38")

# the threshold for displaying labels can be set using the `labelTrheshold` parameter
man <- manhattan(rvbresults[rvbresults$varSetName == "ModerateImpact" & rvbresults$test == "firth",],
                 label = "unit", 
                 labelRepel = TRUE,
                 labelThreshold = 1e-12,
                 contigs = "GRCh38")