from_input_to_profile: Create data for plotting profiles (from raw input to final...

In trvinh/test: PhyloProfile

Description

Create data needed for plotting phylogenetic profile from raw input file.

Usage

from_input_to_profile(raw_input, rank_name, ref_taxon, taxa_tree,
    var1_aggregate_by, var2_aggregate_by, percent_cutoff,
    coortholog_cutoff_max, var1_cutoff, var2_cutoff, var1_relation,
    var2_relation, group_by_cat, cat_dt)

Arguments

raw_input	input file (in long, wide, multi-fasta or orthoxml format)
rank_name	taxonomy rank (e.g. "species","phylum",...)
ref_taxon	selected reference taxon
taxa_tree	input taxonomy tree (optional)
var1_aggregate_by	aggregate method for VAR1 (min, max, mean or median)
var2_aggregate_by	aggregate method for VAR2 (min, max, mean or median)
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 and 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

Value

dataframe for generating profile plot

Author(s)

Vinh Tran [e-mail]

See Also

create_long_matrix, get_input_taxa_id, get_input_taxa_name, sort_input_taxa, parse_info_profile, reduce_profile, create_profile_data

Examples

raw_input <- system.file(
    "extdata", "test.main.long", package = "phyloprofile", mustWork = TRUE
)
rank_name <- "class"
ref_taxon <- "Mammalia"
taxa_tree <- NULL
var1_aggregate_by <- "max"
var2_aggregate_by <- "mean"
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
from_input_to_profile(
    raw_input,
    rank_name,
    ref_taxon,
    taxa_tree,
    var1_aggregate_by,
    var2_aggregate_by,
    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.