Run Ordination on a Microbiome Dataset — run_ordination • microbiomedataset

Perform a basic ordination analysis and return an objectized result.

Usage

run_ordination(
  object,
  method = c("PCoA", "PCA"),
  distance_method = c("bray", "jaccard", "euclidean"),
  n_axes = 2
)

Arguments

object: A microbiome_dataset object.
method: Ordination method.
distance_method: Distance method used for PCoA.
n_axes: Number of axes to keep.

Value

A microbiome_ordination object.

Examples

data("global_patterns", package = "microbiomedataset")

x <- run_ordination(global_patterns, method = "PCoA")
class(x)
#> [1] "microbiome_ordination"
#> attr(,"package")
#> [1] "microbiomedataset"
head(x@sample_coord)
#>        Axis.1       Axis.2 sample_id  Primer Final_Barcode
#> 1 -0.12667533 -0.015709044       CL3 ILBC_01        AACGCA
#> 2 -0.14940705 -0.007137804       CC1 ILBC_02        AACTCG
#> 3 -0.10429782 -0.053710244       SV1 ILBC_03        AACTGT
#> 4  0.28543181  0.025755609   M31Fcsw ILBC_04        AAGAGA
#> 5  0.24415649  0.023606010   M11Fcsw ILBC_05        AAGCTG
#> 6 -0.09259285 -0.327628427   M31Plmr ILBC_07        AATCGT
#>   Barcode_truncated_plus_T Barcode_full_length SampleType
#> 1                   TGCGTT         CTAGCGTGCGT       Soil
#> 2                   CGAGTT         CATCGACGAGT       Soil
#> 3                   ACAGTT         GTACGCACAGT       Soil
#> 4                   TCTCTT         TCGACATCTCT      Feces
#> 5                   CAGCTT         CGACTGCAGCT      Feces
#> 6                   ACGATT         CGAGTCACGAT       Skin
#>                                  Description   class
#> 1   Calhoun South Carolina Pine soil, pH 4.9 Subject
#> 2   Cedar Creek Minnesota, grassland, pH 6.1 Subject
#> 3 Sevilleta new Mexico, desert scrub, pH 8.3 Subject
#> 4    M3, Day 1, fecal swab, whole body study Subject
#> 5   M1, Day 1, fecal swab, whole body study  Subject
#> 6    M3, Day 1, right palm, whole body study Subject