Result Detail – Ordination Help

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Notebook

Method: PCA
Components: 3
Rows ordinated: 35 (61 rows dropped for missing values)
Feature columns: ENV_SOILNH4, ENV_SOILNO3, ENV_SOILP, ENV_SOILOC, ENV_SOILTN, ENV_SOILTC, ENV_PH, ENV_SOILCLAY, ENV_SOILSILT, ENV_SOILSAND, ENV_SOILMOIS, PC_SHOOTMASS, PC_ROOTMASS, PC_LITTERMASS, COVER_TOTAL_JUL, COVER_SHANNON_JUL, SOIL_EC_uS_cm, SOIL_CO2_mg_per_g, BACTERIAL_NECROMASS_C, FUNGAL_NECROMASS_C, MICROBIAL_NECROMASS_C
Warnings: Excluded identifier-like numeric column(s): PLOT. These look like bookkeeping fields rather than measurements. Select feature columns explicitly if you intended to include them.

Ordination scores (axes 1–2) Download PNG

Scree plot Download PNG

Top feature loadings Download PNG

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Method & Provenance

Method: Ordination — PCA
Method key: pca (result type: ordination, result #51)
Engine: Python · scikit-learn v1.8.0
Dataset(s): #702 gallery — catg_example_07_microbial_soil_biology.csv
Status: completed
Permanent link: https://cat-g-omxpert.wishartlab.com/results/by-token/fb6cf1f402b54feeabd9bf3da95b64e6 Bookmark or share this URL — it does not depend on your session.
Created: 2026-09-21 02:15:57.280156

Parameter	Value
`ordination_method`	pca
`method`	pca
`feature_cols`	ENV_SOILNH4, ENV_SOILNO3, ENV_SOILP, ENV_SOILOC, ENV_SOILTN, ENV_SOILTC, ENV_PH, ENV_SOILCLAY, ENV_SOILSILT, ENV_SOILSAND, ENV_SOILMOIS, PC_SHOOTMASS, PC_ROOTMASS, PC_LITTERMASS, COVER_TOTAL_JUL, COVER_SHANNON_JUL, SOIL_EC_uS_cm, SOIL_CO2_mg_per_g, BACTERIAL_NECROMASS_C, FUNGAL_NECROMASS_C, MICROBIAL_NECROMASS_C
`n_components`	3

Reconstructed from the parameters stored with this result — represents the Python/R calls the analysis service made.

from sklearn.decomposition import PCA

from sklearn.preprocessing import StandardScaler

X_scaled = StandardScaler().fit_transform(X)

coords = PCA(n_components=3).fit_transform(X_scaled)