distri_1_taxa: Distribution of sequences across a factor for one taxon

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Distribution of sequences across a factor for one taxon

Description

Focus on one taxon and one factor.

Usage

distri_1_taxa(physeq, fact, taxa_name, digits = 2)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required) Name of the factor in physeq@sam_data used to plot different lines
taxa_name	(required): the name of the taxa
digits	(default = 2) integer indicating the number of decimal places to be used (see ?round for more information)

Value

a dataframe with levels as rows and information as column :

• the number of sequences of the taxa (nb_seq)

• the number of samples of the taxa (nb_samp)

• the mean (mean_nb_seq) and standard deviation (sd_nb_seq) of the nb_seq

• the mean (mean_nb_seq_when_present) nb_seq excluding samples with zero

• the total number of samples (nb_total_samp)

• the proportion of samples with the taxa

Author(s)

Adrien Taudière

Examples

distri_1_taxa(data_fungi, "Height", "ASV2")
distri_1_taxa(data_fungi, "Time", "ASV81", digits = 1)

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.