mapping_contig: Mapping contig
In INRA-LPGP/radsex-vis: Visualization of results from the RADSex pipeline

Description Usage Arguments Examples

Generates a linear plot of RADSex mapping results for a specified contig. The resulting figure contains two plot: the top plot shows sex-bias against position on the contig, and the bottom plot shows probability of association with sex against position on the contig. A specific region of the contig can also be plotted.

mapping_contig(data, contig, region = NULL, title = NULL,
  signif.threshold = 0.05, point.size = 1.5, color.sex.bias = TRUE,
  sex.bias.palette = c("firebrick1", "grey10", "dodgerblue2"),
  association.color = "grey20", significance.line.color = "black",
  significance.line.type = 2, significance.text.position = c(0.05,
  0.05))

`data`	A list of mapping results obtained with the `load_mapping_results` function.
`contig`	Name of the contig to plot.
`region`	A vector of two integers specifying the region of the contig to plot (default NULL).
`title`	Title of the plot (default NULL).
`signif.threshold`	Significance threshold for association with sex (default 0.05).
`point.size`	Size of a point in the plot (default 1.5).
`color.sex.bias`	If TRUE, points on the sex-bias track will be colored according to sex.bias.palette (default TRUE).
`sex.bias.palette`	A vector of three colors defining the sex-bias track palette: female-biased, neutral, male-biased. (default c("firebrick1", "black", "dodgerblue2"))
`association.color`	Color of the points in association with sex plot (default "grey20").
`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)).

1
2
3

data <- load_mapping_results("mapping_results.tsv", contig_lengths_file_path = 'contig_lengths.tsv',
                             contig_names_file_path = 'contig_names.tsv')
#' contig_plot <- mapping_contig(data, "LG05", region = c(1500000, 2500000), point.size = 1, color.sex.bias = FALSE)