Marker Admixture

Associated Constructors

Marker Admixture

Syntax: Marker Admixture( Marker( columns ) )

Description: Estimates population admixture for individuals based on marker genotypes.

JMP Version Added: 19

Example 1

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );

Example 2

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Set(
        Missing Marker Imputation Method( "Specified" ),
        Estimation Method( "Fixed Parameter" ),
        Unthreaded( 1 ),
        Imputation Value( 1 ),
        Number of Ancestral Populations( 3 )
    ),
    Fit(
        Missing Marker Imputation Method( "Specified" ),
        Estimation Method( "Fixed Parameter" ),
        Unthreaded( 1 ),
        Imputation Value( 1 ),
        Number of Ancestral Populations( 3 )
    )
);

Columns

By

Syntax: obj << By( column(s) )

Description: For each level of the specified column, analyzes and presents the results in separate tables and reports.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );

    //Run platform
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), By( :Sex ), Fit );

Label

Syntax: obj << Label( column )

Description: Specifies a column that contains label for each sample.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );

//Run platform
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Label( :Sex ), Fit );

Marker

Syntax: obj << Marker( column(s) )

Description: Specifies columns that contain genetic markers.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );

//Run platform
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Sample ID( :SampleID ),
    Label( :Sex ),
    Fit
);

Sample ID

Syntax: obj << Sample ID( column )

Description: Specifies a column that contains a unique identifier for each sample.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );

//Set up ID Column
dt << New Column( "SampleID",
    Character,
    "Nominal",
    Formula( Char( :Pedigree ) || Char( :Sample ) )
);

//Run platform
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Sample ID( :SampleID ),
    Label( :Sex ),
    Fit
);

Item Messages

Compare

Syntax: obj << Compare

Description: Updates the Marker Admixture comparison metrics.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit,
    Fit( Estimation Method( "Fixed Parameter" ), Number of Ancestral Populations( 3 ) ),
    Set( Estimation Method( "Fixed Parameter" ), Number of Ancestral Populations( 3 ) )
);
obj << Compare( LogLikehood( 0 ) );

Fit

Syntax: obj << Fit

Description: Fits a Marker Admixture model. You can specify parameters and fitting specifications within this command.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Estimation Method( "Fixed Parameter" ),
        Number of Ancestral Populations( 3 ),
        Unthreaded( 1 ),
        Missing Marker Imputation Method( "Specified" ),
        Imputation Value( 1 )
    )
);

Get Measures

Syntax: obj << Get Measures

JMP Version Added: 19

Set

Syntax: obj << Set

Description: Specifies parameters for a Marker Admixture model.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Set(
        Estimation Method( "Fixed Parameter" ),
        Number of Ancestral Populations( 3 ),
        Unthreaded( 1 ),
        Missing Marker Imputation Method( "Specified" ),
        Imputation Value( 1 )
    )
);

Shared Item Messages

Action

Syntax: obj << Action

Description: All-purpose trapdoor within a platform to insert expressions to evaluate. Temporarily sets the DisplayBox and DataTable contexts to the Platform.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Bivariate(
    Y( :height ),
    X( :weight ),
    Action( Distribution( Y( :height, :weight ), Histograms Only ) )
);

Apply Preset

Syntax: Apply Preset( preset ); Apply Preset( source, label, <Folder( folder {, folder2, ...} )> )

Description: Apply a previously created preset to the object, updating the options and customizations to match the saved settings.

JMP Version Added: 18

Anonymous preset

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ), t Test( 1 ) );
preset = obj << New Preset();
dt2 = Open( "$SAMPLE_DATA/Dogs.jmp" );
obj2 = dt2 << Oneway( Y( :LogHist0 ), X( :drug ) );
Wait( 1 );
obj2 << Apply Preset( preset );

Search by name

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ) );
Wait( 1 );
obj << Apply Preset( "Sample Presets", "Compare Distributions" );

Search within folder(s)

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ) );
Wait( 1 );
obj << Apply Preset( "Sample Presets", "t-Tests", Folder( "Compare Means" ) );

Automatic Recalc

Syntax: obj << Automatic Recalc( state=0|1 )

Description: Redoes the analysis automatically for exclude and data changes. If the Automatic Recalc option is turned on, you should consider using Wait(0) commands to ensure that the exclude and data changes take effect before the recalculation.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Automatic Recalc( 1 );
dt << Select Rows( 5 ) << Exclude( 1 );

Broadcast

Syntax: obj << Broadcast(message)

Description: Broadcasts a message to a platform. If return results from individual objects are tables, they are concatenated if possible, and the final format is identical to either the result from the Save Combined Table option in a Table Box or the result from the Concatenate option using a Source column. Other than those, results are stored in a list and returned.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Quality Control/Diameter.jmp" );
objs = Control Chart Builder(
    Variables( Subgroup( :DAY ), Y( :DIAMETER ) ),
    By( :OPERATOR )
);
objs[1] << Broadcast( Save Summaries );

Column Switcher

Syntax: obj << Column Switcher(column reference, {column reference, ...}, < Title(title) >, < Close Outline(0|1) >, < Retain Axis Settings(0|1) >, < Layout(0|1) >)

Description: Adds a control panel for changing the platform's variables

dt = Open( "$SAMPLE_DATA/Car Poll.jmp" );
obj = dt << Contingency( Y( :size ), X( :marital status ) );
ColumnSwitcherObject = obj << Column Switcher(
    :marital status,
    {:sex, :country, :marital status}
);

Copy ByGroup Script

Syntax: obj << Copy ByGroup Script

Description: Create a JSL script to produce this analysis, and put it on the clipboard.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Copy ByGroup Script;

Copy Script

Syntax: obj << Copy Script

Description: Create a JSL script to produce this analysis, and put it on the clipboard.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Copy Script;

Data Table Window

Syntax: obj << Data Table Window

Description: Move the data table window for this analysis to the front.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Data Table Window;

Get By Levels

Syntax: obj << Get By Levels

Description: Returns an associative array mapping the by group columns to their values.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( X( :height ), Y( :weight ), By( :sex ) );
biv << Get By Levels;

Get ByGroup Script

Syntax: obj << Get ByGroup Script

Description: Creates a script (JSL) to produce this analysis and returns it as an expression.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
t = obj[1] << Get ByGroup Script;
Show( t );

Get Container

Syntax: obj << Get Container

Description: Returns a reference to the container box that holds the content for the object.

General

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
t = obj << Get Container;
Show( (t << XPath( "//OutlineBox" )) << Get Title );

Platform with Filter

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
gb = Graph Builder(
    Show Control Panel( 0 ),
    Variables( X( :height ), Y( :weight ) ),
    Elements( Points( X, Y, Legend( 1 ) ), Smoother( X, Y, Legend( 2 ) ) ),
    Local Data Filter(
        Add Filter(
            columns( :age, :sex, :height ),
            Where( :age == {12, 13, 14} ),
            Where( :sex == "F" ),
            Where( :height >= 55 ),
            Display( :age, N Items( 6 ) )
        )
    )
);
New Window( "platform boxes",
    H List Box(
        Outline Box( "Report(platform)", Report( gb ) << Get Picture ),
        Outline Box( "platform << Get Container", (gb << Get Container) << Get Picture )
    )
);

Get Data Table

Syntax: obj << Get Data Table

Description: Returns a reference to the data table.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
t = obj << Get Datatable;
Show( N Rows( t ) );

Get Group Platform

Syntax: obj << Get Group Platform

Description: Return the Group Platform object if this platform is part of a Group. Otherwise, returns Empty().

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( Y( :weight ), X( :height ), By( :sex ) );
group = biv[1] << Get Group Platform;
Wait( 1 );
group << Layout( "Arrange in Tabs" );

Get Script

Syntax: obj << Get Script

Description: Creates a script (JSL) to produce this analysis and returns it as an expression.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
t = obj << Get Script;
Show( t );

Get Script With Data Table

Syntax: obj << Get Script With Data Table

Description: Creates a script(JSL) to produce this analysis specifically referencing this data table and returns it as an expression.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
t = obj << Get Script With Data Table;
Show( t );

Get Timing

Syntax: obj << Get Timing

Description: Times the platform launch.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
t = obj << Get Timing;
Show( t );

Get Web Support

Syntax: obj << Get Web Support

Description: Return a number indicating the level of Interactive HTML support for the display object. 1 means some or all elements are supported. 0 means no support.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Bivariate( Y( :Weight ), X( :Height ) );
s = obj << Get Web Support();
Show( s );

Get Where Expr

Syntax: obj << Get Where Expr

Description: Returns the Where expression for the data subset, if the platform was launched with By() or Where(). Otherwise, returns Empty()

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( X( :height ), Y( :weight ), By( :sex ) );
biv2 = dt << Bivariate( X( :height ), Y( :weight ), Where( :age < 14 & :height > 60 ) );
Show( biv[1] << Get Where Expr, biv2 << Get Where Expr );

Ignore Platform Preferences

Syntax: Ignore Platform Preferences( state=0|1 )

Description: Ignores the current settings of the platform's preferences. The message is ignored when sent to the platform after creation.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Bivariate(
    Ignore Platform Preferences( 1 ),
    Y( :height ),
    X( :weight ),
    Action( Distribution( Y( :height, :weight ), Histograms Only ) )
);

Local Data Filter

Syntax: obj << Local Data Filter

Description: To filter data to specific groups or ranges, but local to this platform

dt = Open( "$SAMPLE_DATA/Car Poll.jmp" );
dt << Distribution(
    Nominal Distribution( Column( :country ) ),
    Local Data Filter(
        Add Filter( columns( :sex ), Where( :sex == "Female" ) ),
        Mode( Show( 1 ), Include( 1 ) )
    )
);

New JSL Preset

Syntax: New JSL Preset( preset )

Description: For testing purposes, create a preset directly from a JSL expression. Like <<New Preset, it will return a Platform Preset that can be applied using <<Apply Preset. But it allows you to specify the full JSL expression for the preset to test outside of normal operation. You will get an Assert on apply if the platform names do not match, but that is expected.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :Height ), X( :Age ) );
preset = obj << New JSL Preset( Oneway( Y( :A ), X( :B ), Each Pair( 1 ) ) );
Wait( 1 );
obj << Apply Preset( preset );

New Preset

Syntax: obj = New Preset()

Description: Create an anonymous preset representing the options and customizations applied to the object. This object can be passed to Apply Preset to copy the settings to another object of the same type.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ), t Test( 1 ) );
preset = obj << New Preset();

Paste Local Data Filter

Syntax: obj << Paste Local Data Filter

Description: Apply the local data filter from the clipboard to the current report.

dt = Open( "$SAMPLE_DATA/Cities.jmp" );
dist = Distribution( Continuous Distribution( Column( :POP ) ) );
filter = dist << Local Data Filter(
    Add Filter( columns( :Region ), Where( :Region == "MW" ) )
);
filter << Copy Local Data Filter;
dist2 = Distribution( Continuous Distribution( Column( :Lead ) ) );
Wait( 1 );
dist2 << Paste Local Data Filter;

Redo Analysis

Syntax: obj << Redo Analysis

Description: Rerun this same analysis in a new window. The analysis will be different if the data has changed.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Redo Analysis;

Redo ByGroup Analysis

Syntax: obj << Redo ByGroup Analysis

Description: Rerun this same analysis in a new window. The analysis will be different if the data has changed.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Redo ByGroup Analysis;

Relaunch Analysis

Syntax: obj << Relaunch Analysis

Description: Opens the platform launch window and recalls the settings that were used to create the report.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Relaunch Analysis;

Relaunch ByGroup

Syntax: obj << Relaunch ByGroup

Description: Opens the platform launch window and recalls the settings that were used to create the report.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Relaunch ByGroup;

Remove Column Switcher

Syntax: obj << Remove Column Switcher

Description: Removes the most recent Column Switcher that has been added to the platform.

dt = Open( "$SAMPLE_DATA/Car Poll.jmp" );
obj = dt << Contingency( Y( :size ), X( :marital status ) );
ColumnSwitcherObject = obj << Column Switcher(
    :marital status,
    {:sex, :country, :marital status}
);
Wait( 2 );
obj << Remove Column Switcher;

Remove Local Data Filter

Syntax: obj << Remove Local Data Filter

Description: If a local data filter has been created, this removes it and restores the platform to use all the data in the data table directly

dt = Open( "$SAMPLE_DATA/Car Poll.jmp" );
dist = dt << Distribution(
    Nominal Distribution( Column( :country ) ),
    Local Data Filter(
        Add Filter( columns( :sex ), Where( :sex == "Female" ) ),
        Mode( Show( 1 ), Include( 1 ) )
    )
);
Wait( 2 );
dist << remove local data filter;

Render Preset

Syntax: Render Preset( preset )

Description: For testing purposes, show the platform rerun script that would be used when applying a platform preset to the platform in the log. No changes are made to the platform.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :Height ), X( :Age ) );
obj << Render Preset( Expr( Oneway( Y( :A ), X( :B ), Each Pair( 1 ) ) ) );

Report

Syntax: obj << Report;Report( obj )

Description: Returns a reference to the report object.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
r = obj << Report;
t = r[Outline Box( 1 )] << Get Title;
Show( t );

Report View

Syntax: obj << Report View( "Full"|"Summary" )

Description: The report view determines the level of detail visible in a platform report. Full shows all of the detail, while Summary shows only select content, dependent on the platform. For customized behavior, display boxes support a <<Set Summary Behavior message.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Report View( "Summary" );

Save ByGroup Script to Data Table

Syntax: Save ByGroup Script to Data Table( <name>, < <<Append Suffix(0|1)>, < <<Prompt(0|1)>, < <<Replace(0|1)> );

Description: Creates a JSL script to produce this analysis, and save it as a table property in the data table. You can specify a name for the script. The Append Suffix option appends a numeric suffix to the script name, which differentiates the script from an existing script with the same name. The Prompt option prompts the user to specify a script name. The Replace option replaces an existing script with the same name.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Save ByGroup Script to Data Table;

Save ByGroup Script to Journal

Syntax: obj << Save ByGroup Script to Journal

Description: Create a JSL script to produce this analysis, and add a Button to the journal containing this script.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Save ByGroup Script to Journal;

Save ByGroup Script to Script Window

Syntax: obj << Save ByGroup Script to Script Window

Description: Create a JSL script to produce this analysis, and append it to the current Script text window.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Save ByGroup Script to Script Window;

Save Script for All Objects

Syntax: obj << Save Script for All Objects

Description: Creates a script for all report objects in the window and appends it to the current Script window. This option is useful when you have multiple reports in the window.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Save Script for All Objects;

Save Script for All Objects To Data Table

Syntax: obj << Save Script for All Objects To Data Table( <name> )

Description: Saves a script for all report objects to the current data table. This option is useful when you have multiple reports in the window. The script is named after the first platform unless you specify the script name in quotes.

Example 1

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Save Script for All Objects To Data Table;

Example 2

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << New Column( "_bycol",
    Character,
    Nominal,
    set values( Repeat( {"A", "B"}, N Rows( dt ) )[1 :: N Rows( dt )] )
);
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit(), By( _bycol ) );
obj[1] << Save Script for All Objects To Data Table( "My Script" );

Save Script to Data Table

Syntax: Save Script to Data Table( <name>, < <<Prompt(0|1)>, < <<Replace(0|1)> );

Description: Create a JSL script to produce this analysis, and save it as a table property in the data table.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Save Script to Data Table( "My Analysis", <<Prompt( 0 ), <<Replace( 0 ) );

Save Script to Journal

Syntax: obj << Save Script to Journal

Description: Create a JSL script to produce this analysis, and add a Button to the journal containing this script.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Save Script to Journal;

Save Script to Report

Syntax: obj << Save Script to Report

Description: Create a JSL script to produce this analysis, and show it in the report itself. Useful to preserve a printed record of what was done.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Save Script to Report;

Save Script to Script Window

Syntax: obj << Save Script to Script Window

Description: Create a JSL script to produce this analysis, and append it to the current Script text window.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Save Script to Script Window;

SendToByGroup

Syntax: SendToByGroup( {":Column == level"}, command );

Description: Sends platform commands or display customization commands to each level of a by-group.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Distribution(
    By( :Sex ),
    SendToByGroup(
        {:sex == "F"},
        Continuous Distribution( Column( :weight ), Normal Quantile Plot( 1 ) )
    ),
    SendToByGroup( {:sex == "M"}, Continuous Distribution( Column( :weight ) ) )
);

SendToEmbeddedScriptable

Syntax: SendToEmbeddedScriptable( Dispatch( "Outline name", "Element name", command );

Description: SendToEmbeddedScriptable restores settings of embedded scriptable objects.

dt = Open( "$SAMPLE_DATA/Reliability/Fan.jmp" );
dt << Life Distribution(
    Y( :Time ),
    Censor( :Censor ),
    Censor Code( 1 ),
    <<Fit Weibull,
    SendToEmbeddedScriptable(
        Dispatch(
            {"Statistics", "Parametric Estimate - Weibull", "Profilers", "Density Profiler"},
            {1, Confidence Intervals( 0 ), Term Value( Time( 6000, Lock( 0 ), Show( 1 ) ) )}
        )
    )
);

SendToReport

Syntax: SendToReport( Dispatch( "Outline name", "Element name", Element type, command );

Description: Send To Report is used in tandem with the Dispatch command to customize the appearance of a report.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Distribution(
    Nominal Distribution( Column( :age ) ),
    Continuous Distribution( Column( :weight ) ),
    SendToReport( Dispatch( "age", "Distrib Nom Hist", FrameBox, {Frame Size( 178, 318 )} ) )
);

Sync to Data Table Changes

Syntax: obj << Sync to Data Table Changes

Description: Sync with the exclude and data changes that have been made.

dt = Open( "$SAMPLE_DATA/Cities.jmp" );
dist = Distribution( Continuous Distribution( Column( :POP ) ) );
Wait( 1 );
dt << Delete Rows( dt << Get Rows Where( :Region == "W" ) );
dist << Sync To Data Table Changes;

Title

Syntax: obj << Title( "new title" )

Description: Sets the title of the platform.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
obj << Title( "My Platform" );

Top Report

Syntax: obj << Top Report

Description: Returns a reference to the root node in the report.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Set(), Fit() );
r = obj << Top Report;
t = r[Outline Box( 1 )] << Get Title;
Show( t );

Transform Column

Syntax: obj = <Platform>(... Transform Column(<name>, Formula(<expression>), [Random Seed(<n>)], [Numeric|Character|Expression], [Continuous|Nominal|Ordinal|Unstructured Text], [column properties]) ...)

Description: Create a transform column in the local context of an object, usually a platform. The transform column is active only for the lifetime of the platform.

JMP Version Added: 16

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Distribution(
    Transform Column( "age^2", Format( "Fixed Dec", 5, 0 ), Formula( :age * :age ) ),
    Continuous Distribution( Column( :"age^2"n ) )
);

View Web XML

Syntax: obj << View Web XML

Description: Returns the XML code that is used to create the interactive HTML report.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Bivariate( Y( :Weight ), X( :Height ) );
xml = obj << View Web XML;

Window View

Syntax: obj = Marker Admixture(...Window View( "Visible"|"Invisible"|"Private" )...)

Description: Set the type of the window to be created for the report. By default a Visible report window will be created. An Invisible window will not appear on screen, but is discoverable by functions such as Window(). A Private window responds to most window messages but is not discoverable and must be addressed through the report object

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( Window View( "Private" ), Y( :weight ), X( :height ), Fit Line );
eqn = Report( biv )["Linear Fit", Text Edit Box( 1 )] << Get Text;
biv << Close Window;
New Window( "Bivariate Equation",
    Outline Box( "Big Class Linear Fit", Text Box( eqn, <<Set Base Font( "Title" ) ) )
);

Marker Admixture Compare

Associated Constructors

Marker Admixture Compare

Syntax: Marker Admixture Compare

Item Messages

Hide All Models

Syntax: obj << Hide All Models

Description: Hides all models.

JMP Version Added: 19

Iterations

Syntax: obj << Iterations( state=0|1 )

Description: Shows or hides the number of iterations when the factorization algorithm stopped. On by default.

JMP Version Added: 19

Log Likelihood

Syntax: obj << Log Likelihood( state=0|1 )

Description: Shows or hides negative logarithm of the likelihood-based function. On by default.

JMP Version Added: 19

Number of Ancestral Populations

Syntax: obj << Number of Ancestral Populations( state=0|1 )

Description: Shows or hides the number of ancestral populations. On by default.

JMP Version Added: 19

Predictors

Syntax: obj << Predictors( state=0|1 )

Description: Shows or hides the Predictors column. On by default.

JMP Version Added: 19

Remove Hidden Models

Syntax: obj << Remove Hidden Models

Description: Removes all models for which the Show box is not checked.

JMP Version Added: 19

Remove Shown Models

Syntax: obj << Remove Shown Models

Description: Removes all models for which the Show check box is checked and shows the remaining models.

JMP Version Added: 19

Show All Models

Syntax: obj << Show All Models

Description: Shows all models.

JMP Version Added: 19

Tolerance

Syntax: obj << Tolerance( state=0|1 )

Description: Shows or hides the tolerance value (RMSE of estimated individual admixture) when the factorization algorithm stopped. On by default.

JMP Version Added: 19

Marker Admixture Fit

Associated Constructors

Marker Admixture Fit

Syntax: Marker Admixture Fit

Item Messages

Cluster Individuals

Syntax: obj << Cluster Individuals( state=0|1 )

Description: Clusters individuals based on their estimated ancestral population admixture probabilities.

JMP Version Added: 19

Example 1

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Cluster Individuals( 1 ));

Example 2

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit( Cluster Individuals( 1 ) )
);

Cluster Markers

Syntax: obj << Cluster Markers( state=0|1 )

Description: Clusters markers based on their reference allele frequencies estimated on each ancestral population.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Cluster Markers( 1 ));

Copy Parameters to Launch

Syntax: obj << Copy Parameters to Launch

Description: Copies the parameters from this model to the model launch section.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Copy Parameters to Launch());

Estimation Method

Syntax: obj = Marker Admixture Fit(...Estimation Method( "Stability Point"|"Fixed Parameter"="Stability Point" )...)

Description: Specifies the method of estimation for the number of ancestral populations. "Stability Point" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Estimation Method( "Fixed Parameter" ),
        Number of Ancestral Populations( 3 ),
        Unthreaded( 1 ),
        Missing Marker Imputation Method( "Specified" ),
        Imputation Value( 1 )
    )
);

Imputation Value

Syntax: obj = Marker Admixture Fit(...Imputation Value( number=0 )...)

Description: Specifies an integer number from zero to the ploidy for the replacement of missing marker scores. "0" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Set Random Seed( 12345 ),
        Missing Marker Imputation Method( "HWE On" ),
        Imputation Value( 1 )
    )
);

Missing Marker Imputation Method

Syntax: obj = Marker Admixture Fit(...Missing Marker Imputation Method( "HWE Off"|"HWE On"|"Random"|"Specified"="HWE Off" )...)

Description: Specifies one of four types of missing marker imputation methods. "HWE Off" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Set Random Seed( 12345 ),
        Missing Marker Imputation Method( "HWE On" ),
        Imputation Value( 1 )
    )
);

Number of Ancestral Populations

Syntax: obj = Marker Admixture Fit(...Number of Ancestral Populations( number=2 )...)

Description: Specifies the number of ancestral populations. "2" by default.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Estimation Method( "Fixed Parameter" ),
        Number of Ancestral Populations( 3 ),
        Unthreaded( 1 )
    )
);

Order Populations Method

Syntax: obj = Marker Admixture Fit(...Order Populations Method( "Average Admixture"|"Variance Explained"="Average Admixture" )...)

Description: Specifies the method for ordering the columns of the P matrix (m x d, where m = number of genetic markers and d is the number of ancestral populations) and the rows of Q matrix (d x n, where n= number of samples). "Average Admixture" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Estimation Method( "Fixed Parameter" ),
        Order Populations Method( "Variance Explained" ),
        Number of Ancestral Populations( 3 )
    ),
    Set(
        Estimation Method( "Fixed Parameter" ),
        Order Populations Method( "Variance Explained" ),
        Number of Ancestral Populations( 3 )
    )
);

Parallel Plot for Individuals

Syntax: obj << Parallel Plot for Individuals( state=0|1 )

Description: Creates an overlay plot of all individuals based on their ancestral population admixture probabilities.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Parallel Plot for Individuals( 1 ));

Parallel Plot for Markers

Syntax: obj << Parallel Plot for Markers( state=0|1 )

Description: Creates an overlay plot of all markers based on their reference allele frequencies estimated on each ancestral population.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Parallel Plot for Markers( 1 ));

Remove All But This Fit

Syntax: obj << ( Fit[number] << Remove All But This Fit( state=0|1 ) )

Description: Removes the reports and plots for all models except this one.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit,
    Fit( Estimation Method( "Fixed Parameter" ), Number of Ancestral Populations( 3 ) ),
    Set( Estimation Method( "Fixed Parameter" ), Number of Ancestral Populations( 3 ) )
);
Wait( 2 );
obj << (Fit[2] << Remove All But This Fit( 1 ));

Remove Fit

Syntax: obj << ( Fit[number] << Remove Fit( state=0|1 ) )

Description: Removes the entire model report.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Set Random Seed( 12345 ),
        Missing Marker Imputation Method( "HWE On" ),
        Imputation Value( 1 )
    )
);
Wait( 2 );
obj << (Fit[1] << Remove Fit( 1 ));

Save F Table

Syntax: obj << Save F Table

Description: Saves the product of matrices P times Q into a table.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Save F Table());

Save P Table

Syntax: obj << Save P Table

Description: Saves the estimated frequency of the reference allele (P) for each genetic marker into a table.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Save P Table());

Save Q Table

Syntax: obj << Save Q Table

Description: Saves the estimated admixture probabilities (Q) of ancestral populations for each sample into a table.

JMP Version Added: 19

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
obj = dt << Marker Admixture( Marker( Column Group( "Markers" ) ), Fit() );
Wait( 2 );
obj << (Fit[1] << Save Q Table());

Set Random Seed

Syntax: obj = Marker Admixture Fit(...Set Random Seed( number=0 )...)

Description: Sets the random seed to a specific value assuring that all subsequent runs using the same seed are reproducible. "0" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Set Random Seed( 12345 ),
        Missing Marker Imputation Method( "HWE On" ),
        Imputation Value( 1 )
    )
);

Unthreaded

Syntax: obj = Marker Admixture Fit(...Unthreaded( state=0 )...)

Description: Use only the main thread for calculations "0" by default.

dt = Open( "$SAMPLE_DATA/Life Sciences/Genotypes Pedigree.jmp" );
dt << Marker Admixture(
    Marker( Column Group( "Markers" ) ),
    Fit(
        Estimation Method( "Fixed Parameter" ),
        Number of Ancestral Populations( 3 ),
        Unthreaded( 1 )
    )
);