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

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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 tran@bio.uni-frankfurt.de

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

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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.