The LabKey flow module supports importing and exporting analyses as a series of .tsv and supporting files in a zip archive. The format is intended to be simple for tools to reformat the results of an external analysis engine for importing into LabKey. Notably, the analysis definition is not included in the archive, but may be defined elsewhere in a FlowJo workspace gating hierarchy, an R flowCore script, or be defined by some other software package.

• Export an Analysis Archive
• Import an Analysis Archive
• Analysis Archive Format
• Statistics File
• Graphs File
• Compensation File
• Keywords File

Export an Analysis Archive

From the flow Runs or FCSAnalysis grid, you can export the analysis results including the original FCS files, keywords, compensation matrices, and statistics.

• Open the analysis and select the runs to export.
• Select (Export).
• Click the Analysis tab.

• Make the selections you need and click Export.

Import an Analysis Archive

To import a flow analysis archive, perhaps after making changes outside the server to add different statistics, graphs, or other information, follow these steps:

• In the flow folder, Flow Summary web part, click Upload and Import.
• Drag and drop the analysis archive into the upload panel.
• Select the archive and click Import Data.
• In the popup, confirm that Import External Analysis is selected.

• Click Import.

Analysis Archive Format

In brief, the archive format contains the following files:

 <root directory>
 ├─ keywords.tsv
 ├─ statistics.tsv
 │
 ├─ compensation.tsv
 ├─ <comp-matrix01>
 ├─ <comp-matrix02>.xml
 │
 ├─ graphs.tsv
 │
 ├─ <Sample Name 01>/
 │  └─ <graph01>.png
 │  └─ <graph02>.svg
 │
 └─ <Sample Name 02>/
    ├─ <graph01>.png
    └─ <graph02>.pdf

All analysis tsv files are optional. The keywords.tsv file lists the keywords for each sample. The statistics.tsv file contains summary statistic values for each sample in the analysis grouped by population. The graphs.tsv contains a catalog of graph images for each sample where the image format may be any image format (pdf, png, svg, etc.) The compensation.tsv contains a catalog of compensation matrices. To keep the directory listing clean, the graphs or compensation matrices may be grouped into sub-directories. For example, the graph images for each sample could be placed into a directory with the same name as the sample.

Statistics File

Sample Name

Population Name

Statistic Name

The statistic value is a either an integer number or a double. Count stats are integer values >= 0. Percentage stats are doubles in the range 0-100. Other stats are doubles. If the statistic is not present for the given sample and population, it is left blank.

Allowed Statistics

For example, the following are valid statistic names:

• Count
• Robust_CV(<FITC>)
• %ile(<Pacific-Blue>:30)
• %of(Lymphocytes)

Examples

No Grouping: One Row Per Sample and Statistic

Grouped By Sample

Grouped By Sample and Population

Grouped By Sample, Population, and Parameter

Graphs File

The graphs.tsv file is a catalog of plot images generated by the analysis. It is similar to the statistics file and lists the sample name, plot file name, and plot parameters. Currently, the only plot parameters included in the graphs.tsv are the population and x and y axes. The graph.tsv file contains one graph image per row. The population column is encoded in the same manner as in the statistics.tsv file. The graph column is the colon-concatenated x and y axes used to render the plot. Compensated parameters are surrounded with <> angle brackets. (Future formats may split x and y axes into separate columns to ease parsing.) The path is a relative file path to the image (no “.” or “..” is allowed in the path) and the image name is usually just an MD5-sum of the graph bytes.

Multi-sample or multi-plot images are not yet supported.

Compensation File

Keywords File