Distribution of sequences across a factor for one taxon

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

Adrien Taudière

Examples

distri_1_taxa(data_fungi_mini, "Height", "ASV7")
#>        nb_seq nb_samp mean_nb_seq sd_nb_seq mean_nb_seq_when_present
#> High    15911      12      568.25   1947.97                  1325.92
#> Low      3818       6      119.31    522.43                   636.33
#> Middle   6501       9      216.70    638.43                   722.33
#>        nb_total_samp prop_samp
#> High              28      0.43
#> Low               32      0.19
#> Middle            30      0.30
# \donttest{
distri_1_taxa(data_fungi, "Time", "ASV81", digits = 1)
#> Taxa are now in rows.
#>    nb_seq nb_samp mean_nb_seq sd_nb_seq mean_nb_seq_when_present nb_total_samp
#> 0    7387       5       110.3     896.8                   1477.4            67
#> 5      24       5         0.6       1.9                      4.8            38
#> 10     10       3         0.5       1.4                      3.3            21
#> 15      0       0         0.0       0.0                      NaN            36
#>    prop_samp
#> 0        0.1
#> 5        0.1
#> 10       0.1
#> 15       0.0
# }