LabKey modules expose their data to the LabKey query engine in one or more schemas. This page outlines the Flow Module's schema, which is helpful to use as a reference when writing custom Flow queries.

Flow Module

The Flow schema has the following tables in it:

Runs Table

This table shows experiment runs for all three of the Flow protocol steps. It has the following columns:

RowId

A unique identifier for the run. Also, when this column is used in a query, it is a lookup back to the same row in the Runs table. That is, including this column in a query will allow the user to display columns from the Runs table that have not been explicitly SELECTed into the query

Flag

The flag column. It is displayed as an icon which the user can use to add a comment to this run. The flag column is a lookup to a table which has a text column “comment”. The icon appears different depending on whether the comment is null.

Name

The name of the run. In flow, the name of the run is always the name of the directory which the FCS files were found in.

Created

The date that this run was created.

CreatedBy

The user who created this run.

Folder

The folder or project in which this run is stored.

FilePathRoot

(hidden) The directory on the server's file system where this run's data files come from.

LSID

The life sciences identifier for this run.

ProtocolStep

The flow protocol step of this run. One of “keywords”, “compensation”, or “analysis”

RunGroups

A unique ID for this run.

AnalysisScript

The AnalysisScript that was used in this run. It is a lookup to the AnalysisScripts table. It will be null if the protocol step is “keywords”

Workspace

CompensationMatrix

The compensation matrix that was used in this run. It is a lookup to the CompensationMatrices table.

TargetStudy

WellCount

The number of FCSFiles that we either inputs or outputs of this run.

FCSFileCount

CompensationControlCount

FCSAnalysisCount

CompensationMatrices

This table shows all of the compensation matrices that have either been calculated in a compensation protocol step, or uploaded.

It has the following columns in it:

RowId

A unique identifier for the compensation matrix.

Name

The name of the compensation matrix. Compensation matrices have the same name as the run which created them. Uploaded compensation matrices have a user-assigned name.

Flag

A flag column to allow the user to add a comment to this compensation matrix

Created

The date the compensation matrix was created or uploaded.

Protocol

(hidden) The protocol that was used to create this compensation matrix. This will be null for uploaded compensation matrices. For calculated compensation matrices, it will be the child protocol “Compensation”

Run

The run which created this compensation matrix. This will be null for uploaded compensation matrices.

Value

A column set with the values of compensation matrix. Compensation matrix values have names which are of the form “spill(channel1:channel2)”

 In addition, the CompensationMatrices table defines a method Value which returns the corresponding spill value.

The following are equivalent:

CompensationMatrices.Value."spill(FL-1:FL-2) "
CompensationMatrices.Value('spill(FL-1:FL-2)')

The Value method would be used when the name of the statistic is not known when the QueryDefinition is created, but is found in some other place (such as a table with a list of spill values that should be displayed).

FCSFiles

The FCSFiles table lists all of the FCS files in the folder. It has the following columns:

RowId

A unique identifier for the FCS file

Name

The name of the FCS file in the file system.

Flag

A flag column for the user to add a comment to this FCS file on the server.

Created

The date that this FCS file was loaded onto the server. This is unrelated to the date of the FCS file in the file system.

Protocol

(hidden) The protocol step that created this FCS file. It will always be the Keywords child protocol.

Run

The experiment run that this FCS file belongs to. It is a lookup to the Runs table.

Keyword

A column set for the keyword values. Keyword names are case sensitive. Keywords which are not present are null.

Sample

The sample description which is linked to this FCS file. If the user has not uploaded sample descriptions, this column will be hidden, and it will be null. This column is a lookup to the SampleSet table.

 In addition, the FCSFiles table defines a method Keyword which can be used to return a keyword value where the keyword name is determined at runtime.

FCSAnalyses

The FCSAnalyses table lists all of the analyses of FCS files. It has the following columns:

RowId

A unique identifier for the FCSAnalysis

Name

The name of the FCSAnalysis. The name of an FCSAnalysis defaults to the same name as the FCSFile.  This is a setting which may be changed.

Flag

A flag column for the user to add a comment to this FCSAnalysis

Created

The date that this FCSAnalysis was created.

Protocol

(hidden) The protocol step that created this FCSAnalysis. It will always be the Analysis child protocol.

Run

The run that this FCSAnalysis belongs to. Note that FCSAnalyses.Run and FCSAnalyses.FCSFile.Run refer to different runs.

Statistic

A column set for statistics that were calculated for this FCSAnalysis.

Graph

A column set for graphs that were generated for this FCSAnalysis. Graph columns display nicely on LabKey, but their underlying value is not interesting. They are a lookup where the display field is the name of the graph if the graph exists, or null if the graph does not exist.

FCSFile

The FCSFile that this FCSAnalysis was performed on. This is a lookup to the FCSFiles table.

In addition, the FCSAnalyses table defines the methods Graph, and Statistic.

CompensationControls

The CompensationControls table lists the analyses of the FCS files that were used to calculate compensation matrices. Often (as in the case of a universal negative) multiple CompensationControls are created for a single FCS file.

The CompensationControls table has the following columns in it:

RowId

A unique identifier for the compensation control

Name

The name of the compensation control. This is the channel that it was used for, followed by either “+”, or “-“

Flag

A flag column for the user to add a comment to this compensation control.

Created

The date that this compensation control was created.

Protocol

(hidden)

Run

The run that this compensation control belongs to. This is the run for the compensation calculation, not the run that the FCS file belongs to.

Statistic

A column set for statistics that were calculated for this compensation control. The following statistics are calculated for a compensation control:

comp:Count

The number of events in the relevant population.

comp:Freq_Of_Parent

The fraction of events that made it through the last gate that was applied in the compensation calculation. This value will be 0 if no gates were applied to the compensation control.

comp:Median(channelName)

The median value of the channelName

 

Graph

A column set for graphs that were generated for this compensation control. The names of graphs for compensation controls are of the form:

comp(channelName)

or

comp(<channelName>)

The latter is shows the post-compensation graph.

In addition, the CompensationControls table defines the methods Statistic and Graph.

AnalysisScripts

The AnalysisScripts table lists the analysis scripts in the folder. This table has the following columns:

RowId

A unique identifier for this analysis script.

Name

The user-assigned name of this analysis script

Flag

A flag column for the user to add a comment to this analysis script

Created

The date this analysis script was created

Protocol

(hidden)

Run

(hidden)

Analyses

The Analyses table lists the experiments in the folder with the exception of the one named Flow Experiment Runs. This table has the following columns:

RowId

A unique identifier

LSID

(hidden)

Name

 

Hypothesis

 

Comments

 

Created

 

CreatedBy

 

Modified

 

ModifiedBy

 

Container

 

CompensationRunCount

The number of compensation calculations in this analysis. It is displayed as a hyperlink to the list of compensation runs.

AnalysisRunCount

The number of runs that have been analyzed in this analysis. It is displayed as a hyperlink to the list of those run analyses

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