Struct light_phylogeny::Options [−][src]
pub struct Options {Show 23 fields
pub gene_internal: bool,
pub species_internal: bool,
pub clado_flag: bool,
pub species_only_flag: bool,
pub real_length_flag: bool,
pub open_browser: bool,
pub verbose: bool,
pub disp_gene: usize,
pub scale: f32,
pub ratio: f32,
pub rotate: bool,
pub remove: bool,
pub thickness_flag: bool,
pub thickness_thresh: usize,
pub thickness_gene: usize,
pub thickness_disp_score: bool,
pub optimisation: bool,
pub height: f32,
pub width: f32,
pub support: bool,
pub free_living: bool,
pub free_living_shift: bool,
pub uniform: bool,
}
Expand description
Structure Options: these are the drawing options for the svg. Concerning recPhyloXML file, we assume in the documentation that it describes a gene/species reconciliation.
Fields
gene_internal: bool
Display internal gene nodes.
species_internal: bool
Display internal species nodes (recPhyloXML).
clado_flag: bool
Display a cladogramme.
species_only_flag: bool
Only draw the species tree (recPhyloXML).
real_length_flag: bool
Use the real branch length.
open_browser: bool
Open the svg in the browser.
verbose: bool
Verbose mode.
disp_gene: usize
Only draw gene tree number # (recPhyloXML).
scale: f32
Scale to be applied to real branch length.
ratio: f32
Ratio between species pipe tree width and cumulated gene trees width (recPhyloXML).
rotate: bool
Rotate the svg 90 counter clockwise.
remove: bool
Not yet implemented.
thickness_flag: bool
Draw only one transfer to represent redundant transfers (recPhyloXML).
thickness_thresh: usize
Abundance threshold for displaying redundant transfers (recPhyloXML).
thickness_gene: usize
Number of the gene tree to display when displaying redundant transfers as one (recPhyloXML).
thickness_disp_score: bool
Display the abundance of the redundant transfers (recPhyloXML).
optimisation: bool
Optimise species branches left/right orientation in order to minimise transfer crossings (recPhyloXML, under development).
height: f32
Scale to be applied to the heigth of the tree.
width: f32
Width to be applied to the heigth of the tree.
support: bool
Display support.
free_living: bool
Support “free living” species (i.e. not associated to a species of the species tree) in the gene tree(s).
free_living_shift: bool
With free_living option : in case of multriple gene trees, shifting free living trees instead superposing.
uniform: bool
Uniformise the species tree nodes size.