5.6 Scripting Reference

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5.6.1 Project Related Commands

5.6.1.1 Creating a New Project

To create a new project that can later be viewed in GUI mode use the following command. Once you create a project all new ChemTree objects will be added to the project as if you were doing the same operations in GUI mode.

EXAMPLE

ghi.newProject(’Discovery’, ’/projects’ )

SYNTAX

ghi.newProject(’projectName’, ’projectLocation’)

Note that the projectLocation must be an existing folder on your file system and projectName will be a new folder in the projectLocation folder.

5.6.1.2 Creating a Temporary Project

To create a temporary project, use the following command. Projects created with this command will not be saved to disk, and will not be available once the script has completed. This command cannot be used in GUI mode.

Note: Projects created with this command cannot be saved using the saveProject command.

EXAMPLE

ghi.newTempProject()

SYNTAX

ghi.newTempProject()

5.6.1.3 Open an Existing Project

To open a project previously created in either GUI mode or script mode use this command.

EXAMPLE

ghi.openProject(’/projects/Discovery/Discovery.ghp’)

SYNTAX

ghi.openProject(’projectPath/projectName.ghp’)

5.6.1.4 Saving a Project

When you are at a point in your workflow where you want to save the state of the current project use this command.

EXAMPLE

ghi.saveProject()

SYNTAX

ghi.saveProject()

5.6.1.5 Closing a Project

The following command will close the current project without saving the state of the project first. If you want to save the project state first use the saveProject command.

EXAMPLE

ghi.closeProject()

SYNTAX

ghi.closeProject()

5.6.2 General GHI Commands

5.6.2.1 Allowing Viewers to Display

There may be times when you are running a script from and you do not want to see viewers, such as progress dialogs, during the running of script commands. The following command will either suppress or allow the display of GUI viewers while executing scripts. Note that you can turn viewers on and off at any time while running a script and this command only affects scripts that are run from the Scripts menu of a viewer.

EXAMPLE

ghi.enableNewViewers(1)

SYNTAX

ghi.enableNewViewers(0 = false 1 = true)

5.6.2.2 Allowing Log Messages to Be Created

There might be times when you do not want to have logging take place during the execution of script commands, but other times when you do want logging. The following command will either suppress or allow the logging of actions while executing scripts. Note that you can turn logging on and off at any time while running a script.

EXAMPLE

ghi.enableLogging(1)

SYNTAX

ghi.turnOffLogging(0 = false, 1 = true)

5.6.2.3 Display a GUI Message

Sometimes you may want to pop up a GUI based message to report status or other information. This command will take the text parameter and display it in a standard message dialog window.

EXAMPLE

ghi.message("my important message")

SYNTAX

ghi.message("some message")

5.6.2.4 Display a GUI Error Message

When you create a script that uses try/except syntax you can put this command in the except clause and any exception message will be displayed in a GUI error dialog.

EXAMPLE

ghi.error()

SYNTAX

ghi.error()

5.6.2.5 Getting a Specific Navigator Node

When you know a Navigator Node display name or a Navigator Node ID you can retrieve an object representing that Navigator Node. The following command is an overloaded command that takes either an integer for the Node ID or a String for the Node name. When asking for a Navigator Node by ID a single object is returned. When asking for a Navigator Node by name a list of objects is returned because names are not guaranteed to be unique.

EXAMPLE

ghi.getObject(’name’)

SYNTAX

objectList = ghi.getObject(’navigator node display name’)

EXAMPLE

ghi.getObject(ID)

SYNTAX

objectVariable = ghi.getObject(navigator node ID)

5.6.2.6 Getting the Current Navigator Node

Another way to get access to Navigator Nodes it to ask for the currently highlighted Node. If no node is highlighted an error will be displayed otherwise an object representing the current Node will be returned.

EXAMPLE

myVar = ghi.getCurrentObject()

SYNTAX

objectName = ghi.getCurrentObject()

5.6.2.7 Choosing a File

This method will display a dialog window for browsing and selecting a file(s). If a file(s) is selected then a tuple with the complete path to the file(s) is returned. If the dialog is canceled then an empty tuple is returned. There are two required parameters the first defines a file extension mask. For example if you pass in "*.txt" the dialog will only display files that have the .txt extension. The second is the title to be displayed in the dialog’s title bar. The third argument is optional. If you put 1 for the third argument the the file chooser will allow multiple files to be selected. If the third argument is omitted or anything but a one is set the the chooser will default to selecting only a single file.

EXAMPLE

myFilePath = ghi.chooseFile("*.txt", "Choose A File Please", 1)

SYNTAX

file path = ghi.chooseFile(file extension mask, dialog title, allow multiple selection)

5.6.2.8 Choosing a directory

The following method can be used to create a file browser for browsing to, and selecting directories. This method has one required parameter, and takes one optional parameter. The required parameter is the title to be displayed in the dialog’s title bar. The optional parameter specifies the initial working directory of the browser. If this parameter is omitted, then the ChemTree application directory will be used as the initial working directory. If the dialog is cancelled, an empty string will be returned. Otherwise, the path of the selected directory will be returned.

EXAMPLE

myDirectoryPath = ghi.chooseDirectory("Choose A Directory Please", C:/ChemTree/example )

SYNTAX

directory path = ghi.chooseDirectory(dialog title, [initial working directory])

5.6.2.9 Creating a Progress Bar

This method will create a progress bar which can display the progress of a certain task, and be used to signal the cancellation of processes. There are two required arguments for this method. The first argument specifies the text to be displayed on the progress bar. The second argument defines the number of progress increments for the progress bar.

EXAMPLE

myProgressBar = ghi.progressBar(“Please Wait”, 100)

SYNTAX

progress bar = ghi.progressBar(“dialog caption”, total number of progress increments)

5.6.2.10 Setting the Progress Bar’s Progress

The following method allows you to set the progress displayed by the progress bar to the value passed in. This value will be displayed on the progress bar as a percentage based on the proportion of the specified progress to the total number or progress increments. For example, if a progress bar is defined as having 50 progress increments, setting the progress to 10 will cause the progress bar to display 20 percent completion

EXAMPLE

myProgressBar.setProgress(10)

SYNTAX

progressBar.setProgress(progressValue)

5.6.2.11 Checking Whether the Progress Bar Has Been Cancelled

The following function allows you to check whether a user has pressed the cancel button on the progress bar. This information may prove useful when trying to determine whether to stop a process prior to it’s completion. If the progress bar has been cancelled the method returns 1. Otherwise, the method returns 0.

EXAMPLE

variable = myProgressBar.wasCancelled()

SYNTAX

integerVariable = myProgressBar.wasCancelled()

5.6.2.12 Disposing of a Progress Bar When Done

It is good practice to make sure that a progress bar is disposed of when the task is complete. After this method is called, the Progress Bar will no longer show itself and calling methods on the script object will have no effect.

EXAMPLE

myProgressBar.finish()

SYNTAX

myProgressBar.finish()

5.6.2.13 Creating a Status Dialog

This method will create a status dialog which can display messages for a task that can not incrementally update a Progress Bar. This is also useful for brief tasks that do not require the full weight of a Progress Bar. There is one argument for this method, the message to by displayed by the Status Dialog.

EXAMPLE

myStatusDialog = ghi.statusDialog(“Doing something brief”)

SYNTAX

status dialog = ghi.statusDialog(“dialog message”)

5.6.2.14 Setting the Status Dialog’s Message

The following method allows you to change the message displayed by the status dialog. This may be useful when you have a series of tasks and you would like to inform the user which task is currently being worked on. The only argument is the message to update the dialog with.

EXAMPLE

myStatusDialog.setMessage(“Now working on a very hard problem.”)

SYNTAX

statusDialog.setMessage(newMessage)

5.6.2.15 Closing the Status Dialog When Done

To close the status dialog, simply call this method. You should always remember to finish the status dialog that you start and only use one at a time.

EXAMPLE

myStatusDialog.finish()

SYNTAX

myStatusDialog.finish()

5.6.3 Commands Common to All Objects

Some commands are available for all the ChemTree objects that you can access from the Python shell. These commands allow you to control GUI aspects of objects you create in scripting.

5.6.3.1 Change a Navigator Node Name

During the course of a script you could be creating Navigator Node objects that will appear in the Navigator Window the next time you open the project in GUI mode. If the generic names assigned to new Navigator Nodes is not the desired behavior you can change the name with this command.

EXAMPLE

myVariable.setName(’myname’)

SYNTAX

objectName.setName(new navigator node name)

5.6.3.2 Getting a Navigator Node Name

If you need to know the name of a Navigator Node use this command with any Python object that corresponds to a Navigator Node.

EXAMPLE

myVariable = someObject.getName()

SYNTAX

variableName = objectName.getName()

5.6.3.3 Getting a Navigator Node Type

If needed, you can get the Navigator Node type from an object with this command. The command returns a string displaying the object’s type.

EXAMPLE

myVariable.getType()

SYNTAX

objectName.getType()

5.6.3.4 Getting a Navigator Node ID

If needed, you can get the Navigator Node ID from an object with this command. The command returns an integer representing a nodes ID.

EXAMPLE

myVariable.getID()

SYNTAX

objectName.getID()

5.6.3.5 Deleting a Navigator Node

To delete a Navigator Node enter this command in the Python Shell window. If a node can not be deleted, such as the project node or a node that is used to create another node, then a message will be displayed and the node will not be deleted. After entering this command in the Python Shell the variable that represented the node will no longer be valid and any attempt to use it will display a message saying it is no longer valid.

EXAMPLE

myVariable.deleteObject()

SYNTAX

objectName.deleteObject()

5.6.3.6 Closing a Navigator Viewer

To cause the viewer for a Navigator Node to be shut down you can enter this command in the Python Shell window.

EXAMPLE

myNodeVariable.close()

SYNTAX

objectName.close()

5.6.3.7 Showing a Navigator Viewer

To cause the viewer for a Navigator Node to be displayed you can enter this command in the Python Shell window.

EXAMPLE

myNodeVariable.show()

SYNTAX

objectName.show()

5.6.3.8 Finding a Node’s Parent

To get an object that represents a node’s parent enter this command in the Python Shell window and it will return an object representing the parent node. You can use the getType() command to test what type of object is returned.

EXAMPLE

newNodeVariable = myNodeVariable.getParent()

SYNTAX

newObjectName = objectName.getParent()

5.6.3.9 Finding a Node’s Secondary Parent

This command returns an object representing the secondary parent of a node. A secondary parent is another node that was used in combination with the current node’s parent to create the current node. If there is no secondary parent then nothing is returned. You can check the type of secondary parent returned by using the getType() command.

EXAMPLE

newNodeVariable = myNodeVariable.getParentSecondary()

SYNTAX

newObjectName = objectName.getParentSecondary()

5.6.3.10 Getting a Node’s Annotations

This command will returned a string with the current contents of the annotations window.

EXAMPLE

stringVariable = myNodeVariable.getAnnotations()

SYNTAX

newStringName = objectName.getAnnotations()

5.6.3.11 Appending to a Node’s Annotations

This command will append a string to the end of the current contents of the annotations window.

EXAMPLE

myNodeVariable.appendAnnotations("some text")

SYNTAX

objectName.appendAnnotations("some text")

5.6.4 Importing and Loading Data

The following commands allow you to import datasets into your open project.

5.6.4.1 Importing GHD-format DataSets

To import a (“Legacy”) GHD-format dataset, use

EXAMPLE

ss = ghi.importGHD(’/home/mydata.ghd’)

SYNTAX

spreadsheet = ghi.importGHD(path and filename of GHD file)

The resulting spreadsheet is returned, and may be assigned to a variable.

5.6.4.2 Importing HTS Files

This method imports compound data either from an SD file or a combination of an SD file and a CSV file.

The parameters are as follows:

  1. The input SD file.
  2. The SD field name for the compound name, if needed. Leave blank if the compound name is to be found in the "normal place", that is, in the header line of the MOLFILE- format block at the beginning of the compound information. (This field is not used if you are in GUI mode and viewers are enabled.)
  3. Slash-separated field(s) desired to be imported from the SD file. Leave blank if none are needed. (This field is not used if you are in GUI mode and viewers are enabled.)
  4. A user descriptor file. Leave blank if no user descriptor file is to be used.
  5. ’C’ for comma-separated or ’S’ for space-separated user descriptor file. (Leave blank if no descriptor file is being used.)
  6. The minimum number of times the path-length descriptor must appear. Use zero to not use auto-generated path-length descriptors. Omit to use the default value of 5.
  7. "A" to ask for augmented atoms (available with MultiVariate only). Otherwise, omit or leave blank.
  8. Maximum path length to be used, if path lengths are to be converted to binary format (available with MultiVariate only). Omit or use zero otherwise.

EXAMPLE

ss = ghi.importHTS(’c:/ChemTree/example/external.SD’,”,”,’c:/ChemTree/example/external.dat’,’S’,5)

EXAMPLE

ss = ghi.importHTS(’c:/ChemTree/mydata/cancersubset.SD’,”,”,’c:/ChemTree/mydata/cancersubset.csv’,’C’,5,’A’,50)

SYNTAX

spreadsheet = ghi.importHTS(path and file name of SD file,SD field name,SD fields,path and file name of descriptor file,’C’ or ’S’,minimum occurrences of path length descriptor,optional- ’A’ for augmented atoms,optional- maximum path length for binary format)

5.6.5 Creating a New DataSet With Scripting

As you manipulate data in scripting there may be times when you would like to add a new dataset and its corresponding spreadsheet to a project. The following set of commands allows you to construct a dataset from Python lists and add the dataset to a project. The first step is to get a datasetbuilder object using the following command.

5.6.5.1 Getting a Datasetbuilder Object

This command returns a pyspreadsheetbuilder object for use in building new datasets. The first parameter is the display name for the dataset when it is added to the navigator window. The next two parameters are the number of rows and columns respectively. The last column indicates weather you want to add a column of row labels. Note that if you want a column of row labels you must use the addRowLabels command before adding any of you data columns.

EXAMPLE

myBuilder = ghi.startSpreadsheetBuilder("datasetName",10,10,1)

SYNTAX

builderObject = ghi.startSpreadsheetBuilder(dataset name, number of rows, number of columns, add a row label column 1=yes 0=no)

5.6.5.2 Adding Row Labels

If you specified that your dataset will have row labels you must use the following command to add the row label column before you add any data columns. There are two parameters for this command the first is the column header and the second is a Py::List of strings that are the row labels.

EXAMPLE

ssbuilderObject.addRowLabels("myLabels", column data list)

SYNTAX

ssbuilderObject.addRowLabels(column header, Py::List of strings)

5.6.5.3 Adding a Column of Boolean Values

The following command adds a column of boolean values. Note the the Py::List of values should be ints 0 and 1.

EXAMPLE

ssbuilderObject.addBoolColumn("myBools", column data list)

SYNTAX

ssbuilderObject.addBoolColumn(column header, Py::List of 0s and 1s)

5.6.5.4 Adding a Column of Integer Values

The following command adds a column of integer values.

EXAMPLE

ssbuilderObject.addIntColumn("myInts", column data list)

SYNTAX

ssbuilderObject.addIntColumn(column header, Py::List of integers)

5.6.5.5 Adding a Column of Double Values

The following command adds a column of double values.

EXAMPLE

ssbuilderObject.addDoubleColumn("myDoubles", column data list)

SYNTAX

ssbuilderObject.addDoubleColumn(column header, Py::List of doubles)

5.6.5.6 Adding a Column of Nominal Values

The following command adds a column of nominal values.

EXAMPLE

ssbuilderObject.addNominalColumn("myNominals", column data list)

SYNTAX

ssbuilderObject.addNominalColumn(column header, Py::List of strings)

5.6.5.7 Creating the DataSet

After you have added all the columns you desire to the pyssbuilder object you are ready to add the dataset to the current project. This command will add the dataset as a child of the node id you pass in as a parameter and return a spreadsheet object representing the new dataset. Note if no parameter is passed in the builder will default to placing the dataset under the project root node.

EXAMPLE

newSpreadsheetObject = ssbuilderObject.finishSpreadsheet(5)

SYNTAX

newSpreadsheetObject = ssbuilderObject.finishSpreadsheet(nodeID)

5.6.6 Spreadsheet Access and Manipulation

Once you have created a scripting spreadsheet object you can use the following commands to manipulate the spreadsheet. For all the commands listed here the scripting spreadsheet is called ss.

5.6.6.1 Getting the Spreadsheet as a Dictionary

Returns the entire spreadsheet as a dictionary of key value pairs, where the key is a string containing the spreadsheet column label, and the value is a list containing the contents of the spreadsheet column. If there a label column, it is also incorporated as a dictionary entry with its associated column label as its key.

EXAMPLE

dict = ss.asDict()

SYNTAX

dict = ss.asDict()

5.6.6.2 Getting the Spreadsheet as a List of Lists

Returns the entire spreadsheet as a list of column lists. The columns will be listed in spreadsheet column number order. If there is a label column it will be the first column.

EXAMPLE

list = ss.asList()

SYNTAX

list = ss.asList()

5.6.6.3 Getting a Spreadsheet Cell

Returns the spreadsheet entry from row i, column j. Row 0 is the row headers and column 0 is the column headers (if they exist). An invalid row or column index throws a RunTimeError exception.

EXAMPLE

object = ss.cell(rowNum, colNum)

SYNTAX

object = ss.cell(Int i, Int J)

5.6.6.4 Getting a Spreadsheet Column by Column Number

Returns the spreadsheet column values for column i. Column 0 is the column headers (if they exist). An invalid column index throws an exception.

EXAMPLE

list = ss.col(3)

SYNTAX

list = ss.col(conNum)

5.6.6.5 Getting a Spreadsheet Column by Column Name

Returns the spreadsheet column values for the column with a header == name. An invalid name throws an exception.

EXAMPLE

list = ss.col("name")

SYNTAX

list = ss.col("columnName")

5.6.6.6 Determining if a Spreadsheet is a Marker Map

Returns 1 if a spreadsheet is a marker map spreadsheet or 0 otherwise.

EXAMPLE

val = ss.isMarkerMap()

SYNTAX

val = ss.isMarkerMap()

5.6.6.7 Get a Spreadsheet Column Type

Returns the column type as one of the following values.

  • 0 is Binary
  • 1 is Integer
  • 2 is Double
  • 3 is Categorical

EXAMPLE

type = ss.getColType(3)

SYNTAX

type = ss.getColType(column number)

5.6.6.8 Get a Spreadsheet Column State

Returns the column state as one of the following values.

  • 0 is inactive
  • 1 is independent
  • 2 is dependent

EXAMPLE

state = ss.getColState(4)

SYNTAX

state = ss.getColState(column number)

5.6.6.9 Export a Spreadsheet to CSV File

Writes the entire contents of the spreadsheet out to the comma-separated file specified in “fileName”. If an empty string is passed in, then the user is prompted for a file. If an error occurs in writing to the file in GUI mode, ChemTree shows an error message to the user.

EXAMPLE

ss.exportCSV("results.csv")

SYNTAX

ss.exportCSV("fileName.csv")

5.6.6.10 Finding a Column by Name

Searches for a column in the spreadsheet whose column label is equal to “colLabel”. It returns the index of that column, or throws an exception if no such column is found.

EXAMPLE

colNum = ss.findCol("name")

SYNTAX

colNum = ss.findCol("columnName")

5.6.6.11 Finding a Row by Name

Searches for a row in the spreadsheet whose row label is equal to “rowLabel”. It returns the index of that row, or throws an exception if no such row is found. The spreadsheet must have row labels otherwise this routine will throw an exception.

EXAMPLE

rowNum = ss.findRow("name")

SYNTAX

rowNum = ss.findRow("rowName")

5.6.6.12 Invert Row States

The state of all rows is inverted. That is, rows that were formerly active are made inactive, and rows that were formerly inactive are made active. This routine is useful in creating training and test sets.

EXAMPLE

ss.invertRowState()

SYNTAX

ss.invertRowState()

5.6.6.13 Getting the Number of Spreadsheet Columns

Returns the number of columns in the spreadsheet (not including the label column).

EXAMPLE

num = ss.numCols()

SYNTAX

numCols = ss.numCols()

5.6.6.14 Get the Number of Columns in a State

Returns the number of columns in the given state. There are three states: 0=Inactive, 1=Independent, 2=Dependent.

EXAMPLE

numIndependant = ss.numColsState(1)

SYNTAX

num = ss.numColsState(state)

5.6.6.15 Get the Number of Spreadsheet Rows

Returns the number of rows in the spreadsheet (not including the column header row).

EXAMPLE

numRows = ss.numRows()

SYNTAX

numRows = ss.numRows()

5.6.6.16 Get the Number of Rows in a State

Returns the number of rows in the given state. There are two states: 0=Inactive, 1=Active.

EXAMPLE

numActive = ss.numRowsState(1)

SYNTAX

num = ss.numRowsState(state)

5.6.6.17 Randomly Shuffle Rows

Randomly permutes the Rows in the spreadsheet by modifying the sort order at random. Subsequent calls to permuteRows will give new permutations, based on the current random seed.

EXAMPLE

ss.permuteRows()

SYNTAX

ss.permuteRows()

5.6.6.18 Getting a Row of Data

Returns a list of elements of row number i. Row 0 is the header row. Rows 1 and up contain the data elements of the spreadsheet. Note that row access is generally slower than column access. An exception is thrown if an invalid row number is specified.

EXAMPLE

list = ss.row(3)

SYNTAX

list = ss.row(rowNum)

5.6.6.19 Change the State of a Single Column

Sets column i to the specified state. There are three states: 0=Inactive, 1=Independent, 2=Dependent. Other column states remain unchanged.

EXAMPLE

ss.setColState(1,2)

SYNTAX

ss.setColState(colNumber, state)

5.6.6.20 Change the State of a Range of Columns

Sets column low through column high inclusively to the specified state. There are three states: 0=Inactive, 1=Independent, 2=Dependent. Other column states remain unchanged.

EXAMPLE

ss.setColState(1,50,1)

SYNTAX

ss.setColState(lowNum, highNum, state)

5.6.6.21 Setting the State of a Single Row

Sets row i to the specified state. There are two states: 0=Inactive, 1=Active. Other row states remain unchanged.

EXAMPLE

ss.setRowState(3,0)

SYNTAX

ss.setRowState(rowNum,state)

5.6.6.22 Getting the State of a Single Row

Returns the state of row i. There are two states: 0=Inactive, 1=Active.

EXAMPLE

ss.getRowState(3)

SYNTAX

ss.getRowState(rowNum)

5.6.6.23 Setting the State of a Range of Rows

Sets row low through row high inclusively to the specified state. There are two states: 0=Inactive, 1=Active. Other row states remain unchanged.

EXAMPLE

ss.setRowState(1,50,0)

SYNTAX

list = ss.setRowState(lowNum,highNum,state)

5.6.6.24 Randomly set a Number of Rows to a State

At random will set a number of rows to be to the specified state. To inactivate numRandomRows rows, set state=0, to activate numRandomRows rows, set state=1. The other rows will be set to the opposite state.

EXAMPLE

ss.setRowStateRandom(25,0)

SYNTAX

ss.setRowStateRandom(numRows,state)

5.6.6.25 Randomly Set a Percentage of Rows to a State

At random will set a fraction of rows to be to the specified state. This is useful for selecting a certain percentage of the data irregardless of its size. To inactive, set state=0, to activate set state=1. The other rows will be set to the opposite state.

EXAMPLE

ss.setRowStateRandom(.5,0)

SYNTAX

ss.setRowStateRandom(percent, state)

5.6.6.26 Sort a Column in Ascending Order

Sorts the spreadsheet by column i in ascending order.

EXAMPLE

ss.sortByColAscending(3)

SYNTAX

ss.sortByColAscending(colNum)

5.6.6.27 Sort a Column in Descending Order

Sorts the spreadsheet by column i in descending order.

EXAMPLE

ss.sortByColDescending(3)

SYNTAX

ss.sortByColDescending(colNum)

5.6.6.28 Remembering a Spreadsheet Page

When you start to make a change to a spreadsheet which has another viewer dependent on it, such as a tree model, the spreadsheet will actually be copied first. The change will then be made on the copy, rather than the original. For convenience’s sake, your spreadsheet variable will always catch up with the spreadsheet change. However, there are times when, after making such a change, you will want to reference the original spreadsheet page.

To make this easier, use the following command before making the spreadsheet change (on “ss” in this example):

EXAMPLE

origSS = ss.thisPage()

SYNTAX

newSheetVariable = current spreadsheet object.thisPage()

Alternatively, you may wish to make the changes using the new spreadsheet variable (“newSS” in the following example) after executing this command the following way:

EXAMPLE

newSS = ss.thisPage()

5.6.7 Using the P-Value plot

Once you have created a P-Value plot object, there are a number of funcions which can be run with that object.

5.6.7.1 Getting P-Values

Use this command to get a python dictionary containing P, aP, and bP values. The dictionary contains the following keys:

  • P
  • aP
  • bP

EXAMPLE

dictionary = myPVPlot.pValue(9)

SYNTAX

dictionary = current P-Value object.pValue(column number)

5.6.7.2 Getting Simes P-Values

Use this command to get a python dictionary containing Simes P, and Simes aP values from a P-Value plot which is ordered by variable number. The dictionary contains the following keys:

  • Simes P
  • Simes aP

EXAMPLE

dictionary = myPVPlot.simesValue(9)

SYNTAX

dictionary = current P-Value object.simesValue(column number)

5.6.7.3 Setting the Simes Window

The following command can be used to change the window size used in calculating Simes P-Values.

EXAMPLE

myPVPlot.setSimes(3)

SYNTAX

current P-Value object.setSimes(new window size, must be > 0, odd, and <= number of plot columns)

5.6.7.4 Getting FDR (aP)

To find the false discovery rate for a specific column in a P-Value plot ordered by aP, use the following command.

EXAMPLE

myvariable = myPVPlot.FDRValue(9)

SYNTAX

myvariable = current P-Value object.FDRValue(column number)

5.6.7.5 Getting all P-Values as a spreadsheet

Use this command to get a spreadsheet object which contains P, aP, bP, Simes P, and Simes aP for all columns represented in the current P-Value plot.

EXAMPLE

myspreadsheet = myPVPlot.pvalueSpreadsheet()

SYNTAX

newSpreadsheet = current P-Value object.FDRValue(column number)

5.6.8 Getting and Setting Tree Options

In order to set parameters that affect how trees are built and what values are shown in GUI mode, you must first get a tree options object. This object works like a python dictionary. Each setting is accessed using subscript notation where the name of the setting is put inside the subscript brackets. Each setting is described below with an example showing the subscript notation. To get a tree options object use this command.

EXAMPLE

options = ghi.getTreeOptions()

SYNTAX

optionsVariable = ghi.getTreeOptions()

Once you have an options object you can change and view the parameters using the following commands.

5.6.8.1 Setting the Minimum Elements for Splitting

EXAMPLE

optionsVariable[’minelements’] = 2

SYNTAX

optionsVariable[’minelements’] = desired split size, must be >= 1

5.6.8.2 Viewing the Minimum Elements Setting

EXAMPLE

optionsVariable[’minelements’]

SYNTAX

myVariable = optionsVariable[’minelements’]

5.6.8.3 Setting the Number of Threads

EXAMPLE

optionsVariable[’numthreads’] = 2

SYNTAX

optionsVariable[’numthreads’] = desired number of threads, must be >= 1

5.6.8.4 Viewing the Number of Threads Setting

EXAMPLE

optionsVariable[’numthreads’]

SYNTAX

myVariable = optionsVariable[’numthreads’]

5.6.8.5 Setting the P Threshold

EXAMPLE

optionsVariable[’pthreshold’] = 0.01

SYNTAX

optionsVariable[’pthreshold’] = desired threshold, must be >= 0

5.6.8.6 Viewing the P Threshold Setting

EXAMPLE

optionsVariable[’pthreshold’]

SYNTAX

myVariable = optionsVariable[’pthreshold’]

5.6.8.7 Setting the Pairwise Threshold

EXAMPLE

optionsVariable[’pairwisepthreshold’] = 0.01

SYNTAX

optionsVariable[’pairwisepthreshold’] = desired pairwise threshold, must be >= 0

5.6.8.8 Viewing the Pairwise Threshold Setting

EXAMPLE

optionsVariable[’pairwisepthreshold’]

SYNTAX

myVariable = optionsVariable[’pairwisepthreshold’]

5.6.8.9 Setting the P Threshold Type

EXAMPLE

optionsVariable[’pthresholdtype’] = 2

SYNTAX

optionsVariable[’pthresholdtype’] = desired threshold type, 0 = raw P 1 = adjusted P 2 = bonferonni adjusted P

5.6.8.10 Viewing the P Threshold Type Setting

EXAMPLE

optionsVariable[’pthresholdtype’]

SYNTAX

myVariable = optionsVariable[’pthresholdtype’]

5.6.8.11 Setting the Segmenting Algorithm

EXAMPLE

optionsVariable[’segalgorithm’] = 0

SYNTAX

optionsVariable[’segalgorithm’] = desired algorithm, 0 = exact 1 = approximate

5.6.8.12 Viewing the Segmenting Algorithm

EXAMPLE

optionsVariable[’segalgorithm’]

SYNTAX

myVariable = optionsVariable[’segalgorithm’]

5.6.8.13 Setting the Maximum Segments

EXAMPLE

optionsVariable[’maxsegments’] = 3

SYNTAX

optionsVariable[’maxsegments’] = desired setting, must be >= 2

5.6.8.14 Viewing the Maximum Segments Setting

EXAMPLE

optionsVariable[’maxsegments’]

SYNTAX

myVariable = optionsVariable[’maxsegments’]

5.6.8.15 Setting Linear Regression

EXAMPLE

optionsVariable[’linearregression’] = 0

SYNTAX

optionsVariable[’linearregression’] = desired setting, 0 = off 1 = on

5.6.8.16 Viewing Linear Regression Setting

EXAMPLE

optionsVariable[’linearregression’]

SYNTAX

myVariable = optionsVariable[’linearregression’]

5.6.8.17 Setting Use Missing Values Option

EXAMPLE

optionsVariable[’usemissing’] = 0

SYNTAX

optionsVariable[’usemissing’] = desired setting, 0 = off 1 = on

5.6.8.18 Viewing Use Missing Values Option

EXAMPLE

optionsVariable[’usemissing’]

SYNTAX

myVariable = optionsVariable[’usemissing’]

5.6.8.19 Setting Resample Iterations

EXAMPLE

optionsVariable[’resample_iterations’] = 0

SYNTAX

optionsVariable[’resample_iterations’] = desired setting

5.6.8.20 Viewing Resample Iterations Setting

EXAMPLE

optionsVariable[’resample_iterations’]

SYNTAX

myVariable = optionsVariable[’resample_iterations’]

5.6.9 Creating a Tree Model

To build tree model you must first set the options you want by using the getTreeOptions() command to get an options object then setting the options to desired values. See(5.6.8). This options object is then passed as the first parameter to the buildTreeModel() command. In addition to the options object there are three optional parameters you can specify in any combination.

  1. numtrees=somevalue 100 is default.
  2. randseed=somevalue 12345678 is default.
  3. numsplitters=somevalue 10 is default.

The buildTreeModel command will return a tree model object.

EXAMPLE

myTreeModel = mySS. buildTreeModel(treeOptions,numtrees=50,randseed=7839743,numsplitters=6)

SYNTAX

newTreeModel = mySpreadsheetObject. buildTreeModel(treeOptions,numtrees=val,randseed=val,numsplitters=val)

5.6.10 Importing a Legacy Tree Model

You can import an existing tree model using the following command. The tree model will imported into the project as a child node of the current spreadsheet.

EXAMPLE

myTreeModel = mySS.importLegacyTreeModel(”C:/HelixTree/myProject/myTree.ght”)

SYNTAX

newTreeModel = spreadsheetObject. importLegacyTreeModel(treeFile)

5.6.11 Tree Model Commands

5.6.11.1 Get Variable Frequencies

This command creates a new project spreadsheet with the variable frequencies of a multi-tree model. The new spreadsheet is added to the project as a child of the tree-model and it is also returned as a spreadsheet in the Python shell.

EXAMPLE

spreadsheetVariable = myTreeModel.variableFrequencies()

SYNTAX

myVariable = myTreeModel.variableFrequencies()