ps_getreturns phyloseqinfo_getreturns psExtraInfo objectdist_getreturns distance matrix (or NULL)ord_getreturns ordination object (or NULL)perm_getreturns adonis2() permanova model (or NULL)bdisp_getreturns results of betadisper() (or NULL)otu_getreturns phyloseq otu_table matrix with taxa as columnstt_getreturns phyloseq tax_tabletax_models_getreturns list generated by tax_model or NULLtax_stats_getreturns dataframe generated by tax_models2stats or NULLtaxatree_models_getreturns list generated by taxatree_models or NULLtaxatree_stats_getreturns dataframe generated by taxatree_models2stats or NULLsamdat_tblreturns phyloseq sample_data as a tibble with sample_names as new first column called .sample_name
Usage
ps_get(psExtra, ps_extra, counts = FALSE, warn = TRUE)
dist_get(psExtra, ps_extra)
ord_get(psExtra, ps_extra)
info_get(psExtra, ps_extra)
perm_get(psExtra, ps_extra)
bdisp_get(psExtra, ps_extra)
tax_models_get(psExtra)
tax_stats_get(psExtra)
taxatree_models_get(psExtra)
taxatree_stats_get(psExtra)
otu_get(data, taxa = NA, samples = NA, counts = FALSE, warn = TRUE)
tt_get(data)
samdat_tbl(data, sample_names_col = ".sample_name")Arguments
- psExtra
psExtra S4 class object
- ps_extra
deprecated! don't use this
- counts
should ps_get or otu_get attempt to return counts? if present in object
- warn
if counts = TRUE, should a warning be emitted if counts are not available? set warn = "error" to stop if counts are not available
- data
phyloseq or psExtra
- taxa
subset of taxa to return, NA for all (default)
- samples
subset of samples to return, NA for all (default)
- sample_names_col
name of column where sample_names are put. if NA, return data.frame with rownames (sample_names)
Examples
data("dietswap", package = "microbiome")
psx <- tax_transform(dietswap, "compositional", rank = "Genus")
psx
#> psExtra object - a phyloseq object with extra slots:
#>
#> 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 ]
#>
#> otu_get(counts = TRUE) [ 130 taxa and 222 samples ]
#>
#> psExtra info:
#> tax_agg = "Genus" tax_trans = "compositional"
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 ]
ps_get(psx, counts = TRUE)
#> 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)
#> psExtra info:
#> tax_agg = "Genus" tax_trans = "compositional"
dist_get(psx) # this psExtra has no dist_calc result
#> NULL
ord_get(psx) # this psExtra has no ord_calc result
#> NULL
perm_get(psx) # this psExtra has no dist_permanova result
#> NULL
bdisp_get(psx) # this psExtra has no dist_bdisp result
#> NULL
# these can be returned from phyloseq objects too
otu_get(psx, taxa = 6:9, samples = c("Sample-9", "Sample-1", "Sample-6"))
#> OTU Table: [4 taxa and 3 samples]
#> taxa are columns
#> Allistipes et rel. Anaerobiospirillum Anaerofustis
#> Sample-9 0.0016615239 0 0
#> Sample-1 0.0397210072 0 0
#> Sample-6 0.0008609339 0 0
#> Anaerostipes caccae et rel.
#> Sample-9 0.002729646
#> Sample-1 0.028845017
#> Sample-6 0.001468652
otu_get(psx, taxa = 6:9, samples = c(9, 1, 6), counts = TRUE)
#> OTU Table: [4 taxa and 3 samples]
#> taxa are columns
#> Allistipes et rel. Anaerobiospirillum Anaerofustis
#> Sample-9 14 0 0
#> Sample-1 336 0 0
#> Sample-6 17 0 0
#> Anaerostipes caccae et rel.
#> Sample-9 23
#> Sample-1 244
#> Sample-6 29
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)
#> # A tibble: 222 × 9
#> .sample_name subject sex nationality group sample timepoint
#> <chr> <fct> <fct> <fct> <fct> <chr> <int>
#> 1 Sample-1 byn male AAM DI Sample-1 4
#> 2 Sample-2 nms male AFR HE Sample-2 2
#> 3 Sample-3 olt male AFR HE Sample-3 2
#> 4 Sample-4 pku female AFR HE Sample-4 2
#> 5 Sample-5 qjy female AFR HE Sample-5 2
#> 6 Sample-6 riv female AFR HE Sample-6 2
#> 7 Sample-7 shj female AFR HE Sample-7 2
#> 8 Sample-8 tgx male AFR HE Sample-8 2
#> 9 Sample-9 ufm male AFR HE Sample-9 2
#> 10 Sample-10 nms male AFR HE Sample-10 3
#> # ℹ 212 more rows
#> # ℹ 2 more variables: timepoint.within.group <int>, bmi_group <fct>
samdat_tbl(psx, sample_names_col = "SAMPLENAME")
#> # A tibble: 222 × 9
#> SAMPLENAME subject sex nationality group sample timepoint
#> <chr> <fct> <fct> <fct> <fct> <chr> <int>
#> 1 Sample-1 byn male AAM DI Sample-1 4
#> 2 Sample-2 nms male AFR HE Sample-2 2
#> 3 Sample-3 olt male AFR HE Sample-3 2
#> 4 Sample-4 pku female AFR HE Sample-4 2
#> 5 Sample-5 qjy female AFR HE Sample-5 2
#> 6 Sample-6 riv female AFR HE Sample-6 2
#> 7 Sample-7 shj female AFR HE Sample-7 2
#> 8 Sample-8 tgx male AFR HE Sample-8 2
#> 9 Sample-9 ufm male AFR HE Sample-9 2
#> 10 Sample-10 nms male AFR HE Sample-10 3
#> # ℹ 212 more rows
#> # ℹ 2 more variables: timepoint.within.group <int>, bmi_group <fct>