Result Detail – Ordination Help

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Result Information

Result ID: 56
Type: Ordination
Status: completed
Dataset ID: 721
Created: 2026-09-21 02:18:08.066263

Ordination Result – PCA Help

Method: PCA
Components: 3
Rows ordinated: 149
Feature columns: 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

Explained variance Help

Axis	Fraction	Cumulative
Axis 1	0.3832	0.3832
Axis 2	0.2030	0.5862
Axis 3	0.0991	0.6854

Ordination scatter Help

Figures

Ordination scores (axes 1–2) Download PNG

Scree plot Download PNG

Top feature loadings Download PNG

Pathway Analysis (same dataset) Help

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Method & Provenance

Method: Ordination — PCA
Method key: pca (result type: ordination, result #56)
Engine: Python · scikit-learn v1.8.0
Dataset(s): #721 gallery — cat_g_metabolomics_subset.csv
Status: completed
Permanent link: https://cat-g-omxpert.wishartlab.com/results/by-token/5b04a18a889d41b2a78dc32205a6aefe Bookmark or share this URL — it does not depend on your session.
Created: 2026-09-21 02:18:08.066263

Parameters used

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

Execution trace

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)