reorder_macrosynteny {macrosyntR}

Reorder the mbh_df before plotting

Description

This is a function to reorder an orthologs_df, that was generated with load_orthologs(). It retrieves communities using igraph::cluster_fast_greedy.

Usage

reorder_macrosynteny(
  orthologs_df,
  pvalue_threshold = 0.001,
  keep_only_significant = FALSE,
  keep_sp1_raw_order = FALSE
)

Arguments

orthologs_df

dataframe. mutual best hits with genomic coordinates loaded with load_orthologs()

pvalue_threshold

numeric. threshold for significancy. (default equals 0.001)

keep_only_significant

logical. (default equals FALSE) tells if the non significant linkage groups should be removed. It drastically speeds up the computation when using one highly fragmented genome.

keep_sp1_raw_order

logical. (default equals FALSE) tells if the reordering should be constrained on the species1 and change just the order of the species2

Value

A dataframe object

See Also

load_orthologs()

compute_macrosynteny()

Examples

# basic usage of reorder_macrosynteny : 

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

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

my_orthologs_reordered <- reorder_macrosynteny(my_orthologs)