Wrapper for a Manhattan plot — manhattan

A wrapper function cleans column format for a Manhattan plot

Usage

manhattan_plot(
  data,
  pos,
  phenotype,
  p_value,
  p_value_threshold = 0.05,
  formal_name = NULL,
  coding = NULL,
  phenotype_list = NULL,
  highlight_region = NULL,
  palette_color = NULL,
  coord_ratio = 2500/1
)

Arguments

data,: data.frame, The table working on
pos,: string, the name of column of position of the variant
phenotype,: str, the name of column of phenotype the variant associated to
p_value,: str, the name of column of p-values
p_value_threshold,: float, the threshold for significance, default 0.05
formal_name,: optional str, the name of column of formal name of each variant, if not specified, will use pos
coding,: optional str, (currently not used), the name of column of exonic vs intronic,
phenotype_list,: optional vector of str, the list of phenotypes which is put into consideration
highlight_region,: optional list of vector of str, in list(c(start, end)...) format, the list of highlighted region
palette_color,: list or str, pre-specfied colors used for different phenotypes
coord_ratio,: float, the coordinate ratio for the figure

Value

ggplot2 instance, the Manhattan plot