MS-DIAL Metabolomics Explorer
Input mode
MS-DIAL CSV (run pipeline)
Pre-processed RDS + pheno
MS-DIAL alignment result (.csv)
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Pipeline runs automatically at defaults: blank filter 30%, missingness 80%, TIC norm, half-min imputation, log2, drift correction (if safe).
PCA object (.rds)
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Phenotype file (.csv/.txt) — sName, Class, File type
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Subset to truxilline targets only (targeted PCA)
m/z tolerance (ppm)
RT tolerance (min)
Matches MS-DIAL features to the 15 truxilline targets by m/z and RT.
Plot type
3D PCA
2D PCA
UMAP (2D)
t-SNE (2D)
PC axis 1
PC1
PC2
PC3
PC4
PC5
PC axis 2
PC1
PC2
PC3
PC4
PC5
PC axis 3
PC1
PC2
PC3
PC4
PC5
Show 3D loadings
Loadings display (3D)
Overlay vectors
Separate side-by-side
3D loading scale
PC axis X
PC1
PC2
PC3
PC4
PC5
PC axis Y
PC1
PC2
PC3
PC4
PC5
Show 95% confidence ellipses
Show 2D loadings
Loadings display (2D)
Overlay vectors
Separate plot below
2D loading scale
UMAP n_neighbors
UMAP min_dist
t-SNE perplexity
t-SNE theta
Run HDBSCAN clustering
minPts
Known-class silhouette
Show known-class silhouette
Compute in:
Current plot space (x,y)
Full PCA space (all PCs)
Number of PCs
Show per-class table
Marker size
Show replicate letter on markers
Color palette
Set1 (RColorBrewer)
Dark2 (RColorBrewer)
viridis
plasma
ggplot2 hue
Custom
Custom colors (comma-separated)
Show legend
Legend position
Right
Left
Top
Bottom
Optional labelInfo CSV (Alignment ID, Metabolite name, Ontology)
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Create / Refresh plot
Max loadings shown (top N by |loading|)
Show numeric loading values in hover
Download HTML plot
Explorer
Pipeline QC
Pipeline Log
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HDBSCAN Silhouette
Known-Class Silhouette
Loadings Table
>0.70 strong | 0.50–0.70 reasonable | 0.25–0.50 weak | <0.25 no structure
Per-class summary
Top loadings for the currently selected PC axes. Available for 2D and 3D PCA modes.