CSV Export

Core Feature

This feature is available in all Portrai Explorer deployments.

Export feature data to CSV format for use in external analysis tools, spreadsheets, or archiving.

Accessing CSV Export

CSV export is available from the Explorer sidebar. Each feature column has a download button that provides export options.

1. Open the Explorer extension
2. In the Features tab, find the column you want to export
3. Click the Download icon (↓) next to the column name
4. Select an export option from the dropdown menu

Export Options

When you click the download button, a dropdown menu appears with two options:

Download All Data

Exports the complete dataset for the selected column, regardless of any active subsets.

Download Selected Data

Exports only the data points that pass everything currently applied. This option is:

• Enabled when something narrows the rows (a subset, a cutoff, a lasso selection or a brush region) and at least one row still passes
• Disabled (grayed out) when every row passes, or when none does

TIP

Use "Download selected data" to export specific portions of your data after applying subsets, lasso selections or brush regions. Dimmed points are not included: the export follows what is drawn at full strength, not what is on screen. Right after you change a subset or a selection, wait until the item count in the mode switcher shows the new total before downloading; until then the export still holds the previous points. The same applies to the plot export below.

Supported Column Types

Categorical Columns

Exports category labels for each data point.

Output format:

index,cell_type
AAACCCAAGAAACACT-1,B cell
AAACCCAAGAAACTGT-1,T cell
AAACCCAAGAAAGACA-1,T cell
AAACCCAAGAAAGGCT-1,Macrophage
...

Continuous Columns

Exports numeric values (e.g., gene expression) for each data point.

Output format:

index,CD3E
AAACCCAAGAAACACT-1,0.0
AAACCCAAGAAACTGT-1,2.345
AAACCCAAGAAAGACA-1,1.892
AAACCCAAGAAAGGCT-1,0.0
...

Embedding Columns

Exports X and Y coordinates from projection data (e.g., UMAP, t-SNE, spatial coordinates). Coordinate columns are not listed in the sidebar: export the current projection's coordinates from the map's Export popover (see Image Export).

The two value headers are {coordinate_column} x and {coordinate_column} y. For a coordinate column named UMAP:

Output format:

index,UMAP x,UMAP y
AAACCCAAGAAACACT-1,1.234,5.678
AAACCCAAGAAACTGT-1,2.345,6.789
AAACCCAAGAAAGACA-1,-0.123,4.567
...

File Details

File Naming

Exported files are automatically named based on the column:

• {column_name}.csv

Examples:

• cell_type.csv
• CD3E.csv
• UMAP.csv for a coordinate column named UMAP

A coordinate column's name is shown in the map's Export popover and can differ from the projection's name in the projection selector. Characters that filenames cannot contain are replaced with _.

Index Column

The first column (index) contains:

• Cell/observation IDs if an ID column is configured in the dataset
• Numeric indices (0, 1, 2, ...) if no ID column is available

Encoding

• UTF-8 encoding
• Standard CSV comma delimiters
• Values containing commas, quotes, or newlines are properly escaped

Working with Exported Data

In Excel

1. Double-click the CSV file to open directly, or
2. Use Data > From Text/CSV for more import options
3. Verify columns are detected correctly

In R

data <- read.csv("cell_type.csv")
head(data)

In Python

import pandas as pd
data = pd.read_csv("cell_type.csv")
data.head()

Large Dataset Handling

CSV export uses streaming technology to handle large datasets efficiently:

• Files download progressively as they are generated
• No file size limit imposed by the browser
• Memory-efficient for datasets with millions of points

WARNING

For very large exports, ensure you have sufficient disk space and a stable internet connection.

Plot Data CSV Export

In addition to the per-column export above, every plot in the Plot extension can export the underlying row-level data it visualizes as CSV. This is available for all six plot types: Scatter, Bar, Stacked Bar, Violin, Box, and Dot.

Accessing Plot CSV Export

1. Open the Plot extension and configure a plot
2. Click the Export button (download icon) in the plot panel's titlebar
3. Under Export data as CSV, choose an option:
   • Download All Data - export every row
   • Download Selected Data - export only the rows that pass everything currently applied: the Subset, the cutoff and the selection together. Points a lasso or a brush left out are drawn dimmed rather than hidden, and they are not included. Unlike the per-column export above, this button stays enabled even when nothing is narrowing the data; it then writes the same rows as Download All Data

What's Included

The export contains one row per data point, with an index column (cell/observation ID, or the row index when no ID is configured) followed by the columns the plot actually uses:

Plot type	Exported columns
Scatter	The X and Y axis sources (continuous columns or signature scores)
Bar	The Group By column, plus the aggregated variable (unless the aggregation is a simple count)
Stacked Bar	The Group By column and the Stack By column
Violin	The Group By column and each selected variable
Box	The Group By column and each selected variable
Dot	The Group By column and each selected variable

Plot CSV export becomes available only once the plot's required fields are configured — for example, a Group By column and at least one variable for Violin, Box, and Dot plots.

Categorical columns are written as their human-readable labels (matching the Explorer per-column export), and numeric columns (continuous features or signature scores) are written as raw values. The same UTF-8 encoding, comma escaping, and streaming behavior described above apply.

DEG Analysis Results Export

InSilicoLab Feature

DEG result export is exclusive to Portrai InSilicoLab.

Differential expression analysis results can be exported from the DEG Analysis workspace. See DEG Analysis - Data Table CSV Export for details.

Troubleshooting

Download Button Not Responding

• Ensure the feature data is fully loaded (no loading spinner)
• Try refreshing the page

"Download Selected Data" is Disabled

• The per-column button needs something narrowing the data (a subset, a cutoff, a lasso selection or a brush region) while at least one row still passes
• Apply one of those first, or loosen it if it leaves no rows. The plot export has no such requirement and stays enabled

File Contains Fewer Rows Than Expected

• Check if "Download selected data" was used instead of "Download all data"
• Verify your subset settings

Download Interrupted

• Check your internet connection
• Ensure sufficient disk space
• Try downloading again

Related Topics

• Image Export - Export visualizations as PNG images
• Features - Understanding feature types
• Import Metadata - Edit an exported column and import it back as a new column
• Subset - Subset data before export
• DEG Analysis - DEG results CSV export