mapping_manhattan_plot: Mapping manhattan plot

In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Description

Generates a manhattan plot of association with sex from RADSex mapping results.

Usage

mapping_manhattan_plot(data, point.size = 0.5, signif.threshold = 0.05,
  point.palette = c("dodgerblue3", "darkgoldenrod2"),
  background.palette = c("grey85", "grey100"),
  significance.line.color = "black", significance.line.type = 2,
  significance.text.position = c(0.05, 0.05))

Arguments

data	A list of mapping results obtained with the load_mapping_results function.
point.size	Size of a point in the plot (default 0.5)
signif.threshold	Significance threshold for association with sex (default 0.05).
point.palette	Color palette for the dots (default c("dodgerblue3", "darkgoldenrod2"))
background.palette	Color palette for the background (default c("grey85", "grey100"))
significance.line.color	Color for significance line, set to NULL for no line (default "black").
significance.line.type	Linetype for the significance line, as usually defined in R (default 2).
significance.text.position	X and Y axis offset for the significance text, as fractions of total axis length (default c(0.05, 0.05)).

Examples

data <- load_mapping_results("mapping_results.tsv", "contig_lengths.tsv", contig_names = "contig_names.tsv", plot.unplaced = FALSE)

 mapping_manhattan_plot(data, point.size = 0.5, signif.threshold = 0.05,
                        point.palette = c("dodgerblue3", "darkgoldenrod2"),
                        background.palette = c("grey85", "grey100"),
                        significance.line.color = "black",
                        significance.line.type = 2,
                        significance.text.position = c(0.05, 0.05)

RomainFeron/radsex-vis documentation built on May 23, 2019, 2:48 p.m.