ps_get
returns phyloseq
info_get
returns ps_extra_info object
dist_get
returns distance matrix (or NULL)
ord_get
returns ordination object (or NULL)
perm_get
returns adonis2() permanova model (or NULL)
bdisp_get
returns results of betadisper() (or NULL)
otu_get
returns phyloseq otu_table matrix with taxa as columns
tt_get
returns phyloseq tax_table
samdat_tbl
returns phyloseq sample_data as a tibble,
with sample_names as new first column called .sample_name
ps_get(ps_extra)
dist_get(ps_extra)
ord_get(ps_extra)
info_get(ps_extra)
perm_get(ps_extra)
bdisp_get(ps_extra)
otu_get(data, taxa = NA, samples = NA, counts = FALSE)
tt_get(data)
samdat_tbl(data, sample_names_col = ".sample_name")
ps_extra class object
phyloseq or ps_extra
subset of taxa to return, NA for all (default)
subset of samples to return, NA for all (default)
should otu_get ensure it returns counts? if present in object
name of column where sample_names are put. if NA, return data.frame with rownames (sample_names)
element of ps_extra class object (or NULL)
data("dietswap", package = "microbiome")
psx <- tax_transform(dietswap, "identity", rank = "Genus")
psx
#> ps_extra object - a list with phyloseq and extras:
#>
#> phyloseq-class experiment-level object
#> otu_table() OTU Table: [ 130 taxa and 222 samples ]
#> sample_data() Sample Data: [ 222 samples by 8 sample variables ]
#> tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]
#>
#> ps_extra info:
#> tax_agg = Genus tax_transform = identity
ps_get(psx)
#> phyloseq-class experiment-level object
#> otu_table() OTU Table: [ 130 taxa and 222 samples ]
#> sample_data() Sample Data: [ 222 samples by 8 sample variables ]
#> tax_table() Taxonomy Table: [ 130 taxa by 3 taxonomic ranks ]
info_get(psx)
#> ps_extra info:
#> tax_agg = Genus
#> tax_transform = identity
#> tax_scale = NA
#> distMethod = NA
#> ordMethod = NA
#> constraints = NA
#> conditions = NA
dist_get(psx) # this ps_extra has no dist_calc result
#> NULL
ord_get(psx) # this ps_extra has no ord_calc result
#> NULL
perm_get(psx) # this ps_extra has no dist_permanova result
#> NULL
bdisp_get(psx) # this ps_extra has no dist_bdisp result
#> NULL
# these can be returned from phyloseq objects too
otu_get(psx)[1:6, 1:4]
#> OTU Table: [4 taxa and 6 samples]
#> taxa are columns
#> Actinomycetaceae Aerococcus Aeromonas Akkermansia
#> Sample-1 0 0 0 18
#> Sample-2 1 0 0 97
#> Sample-3 0 0 0 67
#> Sample-4 1 0 0 256
#> Sample-5 0 0 0 21
#> Sample-6 0 0 0 16
tt_get(psx) %>% head()
#> Taxonomy Table: [6 taxa by 3 taxonomic ranks]:
#> Phylum Family
#> Actinomycetaceae "Actinobacteria" "Actinobacteria"
#> Aerococcus "Firmicutes" "Bacilli"
#> Aeromonas "Proteobacteria" "Proteobacteria"
#> Akkermansia "Verrucomicrobia" "Verrucomicrobia"
#> Alcaligenes faecalis et rel. "Proteobacteria" "Proteobacteria"
#> Allistipes et rel. "Bacteroidetes" "Bacteroidetes"
#> Genus
#> Actinomycetaceae "Actinomycetaceae"
#> Aerococcus "Aerococcus"
#> Aeromonas "Aeromonas"
#> Akkermansia "Akkermansia"
#> Alcaligenes faecalis et rel. "Alcaligenes faecalis et rel."
#> Allistipes et rel. "Allistipes et rel."
samdat_tbl(psx) %>% head()
#> # A tibble: 6 × 9
#> .sample_name subject sex nationality group sample timep…¹ timep…² bmi_g…³
#> <chr> <fct> <fct> <fct> <fct> <chr> <int> <int> <fct>
#> 1 Sample-1 byn male AAM DI Sample-1 4 1 obese
#> 2 Sample-2 nms male AFR HE Sample-2 2 1 lean
#> 3 Sample-3 olt male AFR HE Sample-3 2 1 overwe…
#> 4 Sample-4 pku female AFR HE Sample-4 2 1 obese
#> 5 Sample-5 qjy female AFR HE Sample-5 2 1 overwe…
#> 6 Sample-6 riv female AFR HE Sample-6 2 1 obese
#> # … with abbreviated variable names ¹timepoint, ²timepoint.within.group,
#> # ³bmi_group