custom_annoplot: Custom annotation base plot

In k-hench/GenomicOriginsScripts: Provides the R scripts for the paper "Ancestral variation, hybridization and modularity fuel a marine radiation"

Description

custom_annoplot extracts and plots hypoplectrus annotation data

Usage

custom_annoplot(
  ...,
  searchLG,
  xrange,
  genes_of_interest = c(),
  genes_of_sec_interest = c(),
  anno_rown = 3,
  width = 0.1,
  gene_color = "darkgray",
  start,
  end
)

Arguments

...	catch-all parameter to allow excessive parameters through purrr::pmap
searchLG	string, linkage group (eg. "LG08")
xrange	numeric vector of length 2, range of the plotted window
genes_of_interest	vector of strings, genes that receive a label
genes_of_sec_interest	vector of strings (deprecate/legacy)
anno_rown	numeric, number of rows used for gene annotation
width	numeric, width of genes
gene_color	string (color), highlight color for genes
start	numeric, start position of window (bp)
end	numeric, end position of window (bp)

Details

This is a modification of hypogen::hypo_annotation_baseplot(). The highlighting of the outlier area is added and the coloration of genes is simplified to ony a single color.

See Also

Other Figure 5: ax_scl(), cross_spec(), dist_tibble(), distances_tree(), get_clr(), get_dist(), get_gxp_long(), get_isolated_topos(), get_neighbour_topos(), is_isolated(), min_dist(), no_title(), plot_curtain(), plot_fish_zoom(), plot_fst_poptree(), plot_leg(), plot_panel_anno(), plot_panel_delta_dxy(), plot_panel_dxy(), plot_panel_fst(), plot_panel_gxp(), plot_panel_twisst(), prep_data(), theme_panels()

k-hench/GenomicOriginsScripts documentation built on July 24, 2021, 3:05 p.m.