create_profile_data: Create data for plotting the phylogentic profiles

In trvinh/test: PhyloProfile

Description

Create data for plotting the phylogentic profiles

Usage

create_profile_data(superTaxon_data, ref_taxon, percent_cutoff,
    coortholog_cutoff_max, var1_cutoff, var2_cutoff, var1_relation,
    var2_relation, group_by_cat, cat_dt)

Arguments

superTaxon_data	a reduced dataframe contains info for all profiles in the selected taxonomy rank.
ref_taxon	selected reference taxon
percent_cutoff	min and max cutoffs for percentage of species present in a supertaxon
coortholog_cutoff_max	maximum number of co-orthologs allowed
var1_cutoff	min and max cutoffs for var1
var2_cutoff	min anc max cutoffs for var2
var1_relation	relation of var1 ("protein" for protein-protein or "species" for protein-species)
var2_relation	relation of var2 ("protein" for protein-protein or "species" for protein-species)
group_by_cat	group genes by their categories (TRUE or FALSE)
cat_dt	dataframe contains gene categories (optional, NULL if group_by_cat = FALSE or no info provided)

Value

A dataframe ready for generating profile plot.

Author(s)

Vinh Tran [e-mail]

See Also

parse_info_profile and reduce_profile for generating input dataframe, full_processed_profile for a demo full processed profile dataframe

Examples

data("full_processed_profile", package="phyloprofile")
superTaxon_data <- reduce_profile(full_processed_profile)
ref_taxon <- "Mammalia"
percent_cutoff <- c(0.0, 1.0)
coortholog_cutoff_max <- 10
var1_cutoff <- c(0.75, 1.0)
var2_cutoff <- c(0.5, 1.0)
var1_relation <- "protein"
var2_relation <- "species"
group_by_cat <- FALSE
cat_dt <- NULL
create_profile_data(
    superTaxon_data,
    ref_taxon,
    percent_cutoff,
    coortholog_cutoff_max,
    var1_cutoff,
    var2_cutoff,
    var1_relation,
    var2_relation,
    group_by_cat,
    cat_dt
)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.