draw_manhattan_plot: Draw a manhattan plot

In INRA-LPGP/PoolSex-vis: Visualization of results from PSASS

Description

Draw a manhattan plot from the PSASS data

Usage

draw_manhattan_plot(
  data,
  output.file = NULL,
  width = 14,
  height = 8,
  dpi = 300,
  track = "window_fst",
  lg.numbers = FALSE,
  point.size = 0.5,
  point.palette = c("dodgerblue3", "darkgoldenrod2"),
  background.palette = c("grey85", "grey100"),
  depth.type = "absolute",
  min.depth = 10
)

Arguments

data	A PSASS data structure obtained with the load_data_files function.
output.file	Path to an output file in PNG format. If NULL, the plot will be drawn in the default graphic device (default: NULL).
width	Width of the output file if specified, in inches (default: 14).
height	Height of the output file if specified, in inches (default: 8).
dpi	Resolution of the output file if specified, in dpi (default: 300).
track	Track to be plotted. Possible values are "position_fst", "window_fst", "window_snp_males", "window_snp_females", "depth_males", "depth_females" (default: "window_fst").
lg.numbers	If TRUE, chromosomes / LGs will be labeled with numbers instead of names to increase readability (default: FALSE).
point.size	Size of a point in the plot (default 0.5)
point.palette	Color palette for the dots (default c("dodgerblue3", "darkgoldenrod2"))
background.palette	Color palette for the background (default c("grey85", "grey100"))
depth.type	Type of depth to be plotted, either "absolute" or "relative" (default: "absolute").
min.depth	Minimum depth to compute depth ratio. The ratio for positions with depth lower than this value in either sex will be 1 (default: 10).

Examples

draw_manhattan_plot(data, track = "window_fst")

INRA-LPGP/PoolSex-vis documentation built on March 7, 2020, 6:03 p.m.