Data Matrix Visualization Tool

v1.00

Analysis Status

📊 Data Upload

Data Upload

Copy & Paste

Clean Data Matrix File

DIANN Protein Group Matrix

Expected format: DIANN `results.pg*_matrix.tsv` (protein info columns + intensity columns from column 7 onward).

Data Format: TSV or CSV

First row: Column headers

First column: Row IDs

DIANN mode: Use "DIANN Protein Group Matrix" uploader for `results.pg*_matrix.tsv` (intensity starts at column 7).

Meta Table

Note: Meta table is auto-generated from column names. Upload to override.

Editable: Click cells to edit (Sample_ID is read-only)

Batch edit: Ctrl/Cmd+click to multi-select cells in one column, Shift+click for range, or use "Select All Visible (Same Column)".

Heatmap Controls

Cluster Features (Rows) Cluster Samples (Columns) Distance Metric: Linkage Method: Plot Width (px): Plot Height (px): Max Features to Display: Set to 2000–3000 for faster clustering on large data. Max Samples to Display: Data Preprocessing: Log10 Transform Row-wise Z-score Normalization Heatmap Color Scale: Reverse scale (high = cold, low = hot) Layout & Appearance: Main title (optional): Row dendrogram size (% of width): Column dendrogram size (% of height): Margin left (px): Margin right (px):

Heatmap not generated yet

Click "Generate Heatmap" button to create the visualization

PCA Controls

PC to plot on X-axis: PC to plot on Y-axis: Show Column Labels Auto label font/color Label font size (manual): Label color (manual): Auto show arrows Show arrows (manual) Plot Width (px): Plot Height (px): Main title (optional): Max Samples for PCA: Max Features for PCA:

Reducing features significantly speeds up PCA for large datasets

Number of Components: Fast Mode (fewer iterations, faster but less precise)

Performance: Using optimized typed arrays for faster computation. For best speed, reduce features to 200-500.

Data Preprocessing: Log10 Transform Column-wise Z-score Normalization Row-wise Z-score Normalization

PCA plot not generated yet

Click "Generate PCA Plot" button to create the visualization

t-SNE Controls

Perplexity (5–50): Max iterations: Show Column Labels Auto label font/color Label font size (manual): Label color (manual): Auto show arrows Show arrows (manual) Plot Width (px): Plot Height (px): Main title (optional): Max Samples: Max Features:

t-SNE works well for many samples; limit features for speed.

Data Preprocessing: Log10 Transform Column-wise Z-score Normalization

t-SNE plot not generated yet

Click "Generate t-SNE Plot" to create the embedding and scatter plot

📊 Data Upload

Data Upload

Copy & Paste

Clean Data Matrix File

DIANN Protein Group Matrix

Meta Table

📋 Example Meta Data

Upload Meta Table

Copy & Paste

Browse & Load File

Batch Edit Selected Cells

Heatmap Controls

Group Annotations

PCA Controls

Group Annotation Labels

t-SNE Controls

Group Annotation Labels