Ordination Result #56 — Analysis Report
Contents
- ordination (#56) completed
1. Ordination
2026-09-21 02:18:08 · ordination
The first two PCA axes capture 58.6% of the total variance in the data.
| n_components | 3 |
|---|---|
| method | pca |
| n_rows | 149 |
| n_dropped | 0 |
| color_col | Development_stage |
explained variance
| Axis | Fraction | Cumulative |
|---|---|---|
| Axis 1 | 0.38323 | 0.38323 |
| Axis 2 | 0.203001 | 0.586231 |
| Axis 3 | 0.099128 | 0.68536 |
ordination scatter
scree
loadings
Method & Provenance
- Method
- Ordination — PCA
- Engine
- Python · scikit-learn 1.8.0
- Input dataset
- gallery — cat_g_metabolomics_subset.csv
- Started
- 2026-09-21 02:18:08.066263
- Permanent link
- https://cat-g-omxpert.wishartlab.com/results/by-token/5b04a18a889d41b2a78dc32205a6aefe
| Parameter | Value |
|---|---|
| ordination_method | pca |
| method | pca |
| feature_cols | Protein_content_pct, Days_after_flowering, Orientin.1, benzyladenine-9-N-glucoside, (+)-7-epi-12-hydroxy-12-oxojasmonoyl-L-isoleucine.17, apigenin.2, Soyasaponin III.2, (-)-epicatechin, Myricetin.5, N 6-isopentenyladenosine 5ʹ-monophosphate, (+)-epigallocatechin, Myricetin.6, Quercetin.3, (+)-6a-Hydroxymaackiain, (+)-dihydrokaempferol, Myricetin.3, Dihydromyricetin, genistin, glutathione, melatonin, (indol-3-yl)pyruvate.3, Myricetin.2, kaempferol-3-O-β-D-glucopyranoside-7-O-α-L-rhamnopyranoside, Myricetin.8, myricetin, (+)-dihydromyricetin.3, myricetin 3-O-β-D-glucoside.4, Myricetin.4, Epoxyroussoedione, Orientin, myricetin 3-O-β-D-glucoside.2, (+)-7-epi-12-hydroxyjasmonoyl-L-isoleucine.20, (Z)-ω-(methylsulfanyl)nonyl-thiohydroximate, epoxypheophorbide a.3, (+)-7-epi-12-oxojasmonoyl-L-isoleucine.18, myricetin 3-O-β-D-glucoside.5, (2R,3S,4S)-leucodelphinidin, (+)-taxifolin, myricetin 3-O-β-D-glucoside.1, 4-hydroxybenzoate, neophaseate.2, N-hydroxyhexahomomethioniate, quercetin.5, Kaempferol.1, indole-3-carbaldehyde.2, 3-(3,4-dihydroxyphenyl)pyruvate, a jasmonoyl-L-isoleucine.10, trans-zeatin, a jasmonoyl-L-isoleucine.11, Esculetin, (+)-7-epi-12-hydroxyjasmonoyl-L-isoleucine.22, (-)-epicatechin.2, (2-oxindol-3-yl)acetyl-L-aspartate.8, (+)-7-epi-12-hydroxyjasmonoyl-L-isoleucine.17, (+)-7-epi-12-hydroxy-12-oxojasmonoyl-L-isoleucine.13, Zeatin riboside.1, (-)-epigallocatechin, betulinic aldehyde.7, indole.2, (+)-taxifolin.1, gibberellin A53, (2-oxindol-3-yl)acetyl-L-aspartate.2 |
| n_components | 3 |
| color_col | Development_stage |
Command history
# python from sklearn.decomposition import PCA # python from sklearn.preprocessing import StandardScaler # python X_scaled = StandardScaler().fit_transform(X) # python coords = PCA(n_components=3).fit_transform(X_scaled)