Ordination results format (skbio.io.format.ordination)

The ordination results file format (ordination) stores the results of an ordination method in a human-readable, text-based format. The format supports storing the results of various ordination methods available in scikit-bio, including (but not necessarily limited to) PCoA, CA, RDA, and CCA.

Format Support

Has Sniffer: Yes

Reader Writer Object Class
Yes Yes skbio.stats.ordination.OrdinationResults

Format Specification

The format is text-based, consisting of six attributes that describe the ordination results:

  • Eigvals: 1-D
  • Proportion explained: 1-D
  • Species: 2-D
  • Site: 2-D
  • Biplot: 2-D
  • Site constraints: 2-D

The attributes in the file must be in this order.

Each attribute is defined in its own section of the file, where sections are separated by a blank (or whitespace-only) line. Each attribute begins with a header line, which contains the attribute’s name (as listed above), followed by a tab character, followed by one or more tab-separated dimensions (integers) that describe the shape of the attribute’s data.

The attribute’s data follows its header line, and is stored in tab-separated format. Species, Site, and Site constraints store species and site IDs, respectively, as the first column, followed by the 2-D data array.

An example of this file format might look like:

Eigvals<tab>4
0.36<tab>0.18<tab>0.07<tab>0.08

Proportion explained<tab>4
0.46<tab>0.23<tab>0.10<tab>0.10

Species<tab>9<tab>4
Species0<tab>0.11<tab>0.28<tab>-0.20<tab>-0.00
Species1<tab>0.14<tab>0.30<tab>0.39<tab>-0.14
Species2<tab>-1.01<tab>0.09<tab>-0.19<tab>-0.10
Species3<tab>-1.03<tab>0.10<tab>0.22<tab>0.22
Species4<tab>1.05<tab>0.53<tab>-0.43<tab>0.22
Species5<tab>0.99<tab>0.57<tab>0.67<tab>-0.38
Species6<tab>0.25<tab>-0.17<tab>-0.20<tab>0.43
Species7<tab>0.14<tab>-0.85<tab>-0.01<tab>0.05
Species8<tab>0.41<tab>-0.70<tab>0.21<tab>-0.69

Site<tab>10<tab>4
Site0<tab>0.71<tab>-3.08<tab>0.21<tab>-1.24
Site1<tab>0.58<tab>-3.00<tab>-0.94<tab>2.69
Site2<tab>0.76<tab>-3.15<tab>2.13<tab>-3.11
Site3<tab>1.11<tab>1.07<tab>-1.87<tab>0.66
Site4<tab>-0.97<tab>-0.06<tab>-0.69<tab>-0.61
Site5<tab>1.04<tab>0.45<tab>-0.63<tab>0.28
Site6<tab>-0.95<tab>-0.08<tab>0.13<tab>-0.42
Site7<tab>0.94<tab>-0.10<tab>0.52<tab>-0.00
Site8<tab>-1.14<tab>0.49<tab>0.47<tab>1.17
Site9<tab>1.03<tab>1.03<tab>2.74<tab>-1.28

Biplot<tab>3<tab>3
-0.16<tab>0.63<tab>0.76
-0.99<tab>0.06<tab>-0.04
0.18<tab>-0.97<tab>0.03

Site constraints<tab>10<tab>4
Site0<tab>0.69<tab>-3.08<tab>-0.32<tab>-1.24
Site1<tab>0.66<tab>-3.06<tab>0.23<tab>2.69
Site2<tab>0.63<tab>-3.04<tab>0.78<tab>-3.11
Site3<tab>1.10<tab>0.50<tab>-1.55<tab>0.66
Site4<tab>-0.97<tab>0.06<tab>-1.12<tab>-0.61
Site5<tab>1.05<tab>0.53<tab>-0.43<tab>0.28
Site6<tab>-1.02<tab>0.10<tab>-0.00<tab>-0.42
Site7<tab>0.99<tab>0.57<tab>0.67<tab>-0.00
Site8<tab>-1.08<tab>0.13<tab>1.11<tab>1.17
Site9<tab>0.94<tab>0.61<tab>1.79<tab>-1.28

If a given result attribute is not present (e.g. Biplot), it should still be defined and declare its dimensions as 0. For example:

Biplot<tab>0<tab>0

All attributes are optional except for Eigvals.

Examples

Assume we have the following tab-delimited text file storing the ordination results in ordination format:

Eigvals<tab>4
0.36<tab>0.18<tab>0.07<tab>0.08

Proportion explained<tab>4
0.46<tab>0.23<tab>0.10<tab>0.10

Species<tab>9<tab>4
Species0<tab>0.11<tab>0.28<tab>-0.20<tab>-0.00
Species1<tab>0.14<tab>0.30<tab>0.39<tab>-0.14
Species2<tab>-1.01<tab>0.09<tab>-0.19<tab>-0.10
Species3<tab>-1.03<tab>0.10<tab>0.22<tab>0.22
Species4<tab>1.05<tab>0.53<tab>-0.43<tab>0.22
Species5<tab>0.99<tab>0.57<tab>0.67<tab>-0.38
Species6<tab>0.25<tab>-0.17<tab>-0.20<tab>0.43
Species7<tab>0.14<tab>-0.85<tab>-0.01<tab>0.05
Species8<tab>0.41<tab>-0.70<tab>0.21<tab>-0.69

Site<tab>10<tab>4
Site0<tab>0.71<tab>-3.08<tab>0.21<tab>-1.24
Site1<tab>0.58<tab>-3.00<tab>-0.94<tab>2.69
Site2<tab>0.76<tab>-3.15<tab>2.13<tab>-3.11
Site3<tab>1.11<tab>1.07<tab>-1.87<tab>0.66
Site4<tab>-0.97<tab>-0.06<tab>-0.69<tab>-0.61
Site5<tab>1.04<tab>0.45<tab>-0.63<tab>0.28
Site6<tab>-0.95<tab>-0.08<tab>0.13<tab>-0.42
Site7<tab>0.94<tab>-0.10<tab>0.52<tab>-0.00
Site8<tab>-1.14<tab>0.49<tab>0.47<tab>1.17
Site9<tab>1.03<tab>1.03<tab>2.74<tab>-1.28

Biplot<tab>0<tab>0

Site constraints<tab>0<tab>0

Load the ordination results from the file:

>>> from StringIO import StringIO
>>> from skbio.stats.ordination import OrdinationResults
>>> or_f = StringIO(
...  "Eigvals\t4\n"
...  "0.36\t0.18\t0.07\t0.08\n"
...  "\n"
...  "Proportion explained\t4\n"
...  "0.46\t0.23\t0.10\t0.10\n"
...  "\n"
...  "Species\t9\t4\n"
...  "Species0\t0.11\t0.28\t-0.20\t-0.00\n"
...  "Species1\t0.14\t0.30\t0.39\t-0.14\n"
...  "Species2\t-1.01\t0.09\t-0.19\t-0.10\n"
...  "Species3\t-1.03\t0.10\t0.22\t0.22\n"
...  "Species4\t1.05\t0.53\t-0.43\t0.22\n"
...  "Species5\t0.99\t0.57\t0.67\t-0.38\n"
...  "Species6\t0.25\t-0.17\t-0.20\t0.43\n"
...  "Species7\t0.14\t-0.85\t-0.01\t0.05\n"
...  "Species8\t0.41\t-0.70\t0.21\t-0.69\n"
...  "\n"
...  "Site\t10\t4\n"
...  "Site0\t0.71\t-3.08\t0.21\t-1.24\n"
...  "Site1\t0.58\t-3.00\t-0.94\t2.69\n"
...  "Site2\t0.76\t-3.15\t2.13\t-3.11\n"
...  "Site3\t1.11\t1.07\t-1.87\t0.66\n"
...  "Site4\t-0.97\t-0.06\t-0.69\t-0.61\n"
...  "Site5\t1.04\t0.45\t-0.63\t0.28\n"
...  "Site6\t-0.95\t-0.08\t0.13\t-0.42\n"
...  "Site7\t0.94\t-0.10\t0.52\t-0.00\n"
...  "Site8\t-1.14\t0.49\t0.47\t1.17\n"
...  "Site9\t1.03\t1.03\t2.74\t-1.28\n"
...  "\n"
...  "Biplot\t0\t0\n"
...  "\n"
...  "Site constraints\t0\t0\n")
>>> ord_res = OrdinationResults.read(or_f)