plot_curtain: Manage plot panels for a single outlier window

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

Description

plot_curtain calls all individual plotting functions needed for a single outlier zoom

Usage

plot_curtain(
  loc = "bel",
  outlier_id,
  outlier_nr,
  lg,
  start,
  end,
  cool_genes,
  text = TRUE,
  label,
  trait,
  data_tables,
  ...
)

Arguments

loc	string, sample location (bel [Belize]/ hon [Honduras]/ pan [Panama])
outlier_id	string, identifier of fst outlier ID (eg "LG04_1")
outlier_nr	numeric (deprecated)
lg	string, linkage group (eg. "LG08")
start	numeric, start position of window (bp)
end	numeric, end position of window (bp)
cool_genes	vector of strings, genes that receive a label
text	logical, toggle y axis label and ticks
label	string, panel label ("A"/"B"/"C")
trait	string, trait identifier for icon on gxp plot
data_tables	list with twisst results
...	catch-all parameter to allow excessive parameters through purrr::pmap

Details

The panels containg the gene models, fst, dxy delta dxy, genotype x phenotype association and topology weighting are called.

Then they are combined using cowplot::plot_grid and depending on the column position (first column/ other column), the y axis titles are removed.

See Also

Other Figure 5: ax_scl(), cross_spec(), custom_annoplot(), dist_tibble(), distances_tree(), get_clr(), get_dist(), get_gxp_long(), get_isolated_topos(), get_neighbour_topos(), is_isolated(), min_dist(), no_title(), 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.