Visualization of a collection of couples of samples for comparison

This allow to plot all the possible biplot_pq() combination using one factor.

Usage

multi_biplot_pq(physeq, split_by = NULL, pairs = NULL, na_remove = TRUE, ...)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

split_by

(required if pairs is NULL) the name of the factor to make all combination of couples of values

pairs

(required if pairs is NULL) the name of the factor in physeq@sam_data` slot to make plot by pairs of samples. Each level must be present only two times. Note that if you set pairs, you also must set fact arguments to pass on to biplot_pq().

na_remove

(logical, default TRUE) if TRUE remove all the samples with NA in the split_by variable of the physeq@sam_data slot

...

Other parameters passed on to biplot_pq()

Value

a list of ggplot object

Author

Adrien Taudière

Examples

# \donttest{
data_fungi_abun <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 10000)
#> Cleaning suppress 0 taxa (  ) and 15 sample(s) ( BE9-006-B_S27_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / DJ2-008-B_S87_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / E9-009-H_S101_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / O20-X-B_S139_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / R28-008-H_S159_MERGED.fastq.gz / R28-008-M_S160_MERGED.fastq.gz / W26-001-M_S167_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz / Y29-007-M_S183_MERGED.fastq.gz ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 1385
#> Number of kept ASV 35
#> Number of kept samples 170
p <- multi_biplot_pq(data_fungi_abun, "Height")
#> 54 were discarded due to NA in variables present in formula.
#> Cleaning suppress 0 taxa and 0 samples.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
lapply(p, print)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_rect()`).

#> $`High - Low`
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_rect()`).

#> 
# }