plot_chord_diagram {macrosyntR}

plot the Macro-synteny as a chord diagram

Description

This is a function to plot the chord diagrams to compare the macro synteny of two or more species. It requires as input an orthologs_df loaded by load_orthologs()

Usage

plot_chord_diagram(
  orthologs_df,
  species_labels = NULL,
  species_labels_size = 5,
  color_by = "sp1.Chr",
  custom_color_palette = NULL,
  reorder_chromosomes = TRUE,
  remove_non_linkage_orthologs = TRUE,
  species_labels_hpos = -400,
  label_size = 2,
  ideogram_fill = "white",
  ideogram_color = "black",
  ideogram_height = 4,
  ribbons_curvature = 0.1,
  ribbons_alpha = 0.5
)

Arguments

orthologs_df

dataframe. orthologs with genomic coordinates loaded by the load_orthologs()

species_labels

list of characters. names of the species to display on the plot

species_labels_size

integer. size of the labels (default = 2)

color_by

string. name of the column in the orthologs_df to color the links by (default = "sp1.Chr")

custom_color_palette

list of characters. palette to use for the coloring of the links following the argument color_by

reorder_chromosomes

logical. (default = TRUE) tells whether to reorder the chromosomes in clusters as implemented in reorder_macrosynteny()

remove_non_linkage_orthologs

logical. (default = TRUE) tells wether to remove the orthologs that are not within significant linkage groups as calculated by comput_linkage_groups().

species_labels_hpos

(default =-400)

label_size

integer. size of the labels to display on the ideograms (default = 2)

ideogram_fill

character. name of the colors to fill the ideograms with (default = "white")

ideogram_color

character. name of the colors to draw the borders of the ideograms with (default = "black")

ideogram_height

integer. height of the ideograms (default = 4)

ribbons_curvature

float. curvature of the ribbons (default = 0.1)

ribbons_alpha

float. alpha of the ribbons (default = 0.5)

Value

A ggplot2 object

See Also

load_orthologs()

reorder_macrosynteny()

compute_linkage_groups()

Examples

# basic usage of plot_oxford_grid : 

orthologs_table <- system.file("extdata","my_orthologs.tab",package="macrosyntR")

my_orthologs <- read.table(orthologs_table,header=TRUE)

plot_chord_diagram(my_orthologs,species_labels = c("B. flo","P. ech"))