net.maizegenetics.pangenome.hapCalling

Class PathToIgraphPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class PathToIgraphPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Author:

Peter Bradbury The PathToIgraphPlugin exports data for a path and the graph used to generate it from a PHG database. The data is exported in a format that can be imported by the igraph package in R. There is also an igraph package available for Python as well. The export consists of two files for each chromosome, a vertex file and an edge file. The vertex (or node) file contains the following columns: id a sequential id assigned to each node range a sequential id assigned to each reference range according to its position in a chromosome hapid the haplotype_id from the database for each node name the name used to label each node in the graph, set to ntaxa ntaxa the number of taxa in each node inclusion the inclusion count for each node exclusion the exclusion count for each node ispath whether a node is on the path istarget whether the node is contains the target taxon chr the chromosome of the node start the start position of the range end the end position of the range The edge file consists of the following columns: from the id of the node (vertex) from which the edge originates to the id of the node to which the edge connects prob the edge weight. It equals the number of taxa shared in common between the connected nodes divided by the total taxa in common between the adjacent ranges The path is the path imputed by the fastq file used to generate the path. The target taxon is a taxon chosen by the user to compare to the imputed path. The input expected by the Plugin is a HaplotypeGraph, presumably created by HaplotypeGraphBuilderPlugin using the same parameters and database used to impute the path. The other parameters taken by the PathToIgraphPlugin should match parameter values used to create the path.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
PathToIgraphPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	configFile() Database configuration file
PathToIgraphPlugin	configFile(String value) Set Database Config File.
String	countMethod() The haplotype count method name assigned when the counts were created and stored in the DB.
PathToIgraphPlugin	countMethod(String value) Set Haplotype count method name.
String	fastqName() The name of the fastq file used to create the path.
PathToIgraphPlugin	fastqName(String value) Set Fastq name.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	outputBase() base name for output files from this Plugin.
PathToIgraphPlugin	outputBase(String value) Set Output file base.
String	pathName() The path method name assigned when the path was created and stored in the DB.
PathToIgraphPlugin	pathName(String value) Set Path method name.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refRangeFile() The name of the file containing the reference ranges to keep.
PathToIgraphPlugin	refRangeFile(String value) Set Ref Range File.
void	runPlugin(net.maizegenetics.plugindef.DataSet input) Convenience method to run plugin that returns nothing.
Double	splitTransitionProb() When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon.
PathToIgraphPlugin	splitTransitionProb(Double value) Set Split Prob.
PathToIgraphPlugin	taxaFilter(net.maizegenetics.taxa.TaxaList value) Set Taxa.
net.maizegenetics.taxa.TaxaList	taxaFilterString() A list of taxa to include in graph.
String	taxonName() The name of the taxon for which the path is requested.
PathToIgraphPlugin	taxonName(String value) Set Taxon name.
void	writeGraphInfoAllChr(String outbase, int[] pathids, HaplotypeGraph graph, int[][] inclusionExclusionCounts, String target)
void	writeGraphInfoFilesForChr(String outbase, int[] pathids, HaplotypeGraph graph, Map<Integer,Integer> inclusionMap, Map<Integer,Integer> exclusionMap, net.maizegenetics.dna.map.Chromosome chr, String target)

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

PathToIgraphPlugin

public PathToIgraphPlugin(Frame parentFrame,
                          boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

writeGraphInfoAllChr

public void writeGraphInfoAllChr(String outbase,
                                 int[] pathids,
                                 HaplotypeGraph graph,
                                 int[][] inclusionExclusionCounts,
                                 String target)

writeGraphInfoFilesForChr

public void writeGraphInfoFilesForChr(String outbase,
                                      int[] pathids,
                                      HaplotypeGraph graph,
                                      Map<Integer,Integer> inclusionMap,
                                      Map<Integer,Integer> exclusionMap,
                                      net.maizegenetics.dna.map.Chromosome chr,
                                      String target)

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

runPlugin

public void runPlugin(net.maizegenetics.plugindef.DataSet input)

Convenience method to run plugin that returns nothing.

taxonName

public String taxonName()

The name of the taxon for which the path is requested.

Returns:

Taxon name

taxonName

public PathToIgraphPlugin taxonName(String value)

Set Taxon name. The name of the taxon for which the path is requested.

Parameters:

value - Taxon name

Returns:

this plugin

pathName

public String pathName()

The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.

Returns:

Path method name

pathName

public PathToIgraphPlugin pathName(String value)

Set Path method name. The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.

Parameters:

value - Path method name

Returns:

this plugin

countMethod

public String countMethod()

The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.

Returns:

Haplotype count method name

countMethod

public PathToIgraphPlugin countMethod(String value)

Set Haplotype count method name. The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.

Parameters:

value - Haplotype count method name

Returns:

this plugin

fastqName

public String fastqName()

The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.

Returns:

Fastq name

fastqName

public PathToIgraphPlugin fastqName(String value)

Set Fastq name. The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.

Parameters:

value - Fastq name

Returns:

this plugin

configFile

public String configFile()

Database configuration file

Returns:

Database Config File

configFile

public PathToIgraphPlugin configFile(String value)

Set Database Config File. Database configuration file

Parameters:

value - Database Config File

Returns:

this plugin

splitTransitionProb

public Double splitTransitionProb()

When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.

Returns:

Split Prob

splitTransitionProb

public PathToIgraphPlugin splitTransitionProb(Double value)

Set Split Prob. When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.

Parameters:

value - Split Prob

Returns:

this plugin

taxaFilterString

public net.maizegenetics.taxa.TaxaList taxaFilterString()

A list of taxa to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.

Returns:

Taxa

taxaFilter

public PathToIgraphPlugin taxaFilter(net.maizegenetics.taxa.TaxaList value)

Set Taxa. A list of taxa to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.

Parameters:

value - Taxa

Returns:

this plugin

refRangeFile

public String refRangeFile()

The name of the file containing the reference ranges to keep.

Returns:

Ref Range File

refRangeFile

public PathToIgraphPlugin refRangeFile(String value)

Set Ref Range File. The name of the file containing the reference ranges to keep.

Parameters:

value - Ref Range File

Returns:

this plugin

outputBase

public String outputBase()

base name for output files from this Plugin. Two files will be produced for each chromosome.

Returns:

Output file base

outputBase

public PathToIgraphPlugin outputBase(String value)

Set Output file base. base name for output files from this Plugin. Two files will be produced for each chromosome.

Parameters:

value - Output file base

Returns:

this plugin