public VennDiagramData CenterVennDiagramData()
{
// Shift the circles to be centered about zero
VennDiagramData v = new VennDiagramData(this);
v.Center();
return(v);
}
//*************************************************************************
// Method: CreateVennDiagramNodeXLFile()
//
/// <summary>
/// Demonstrates how the NodeXL template can be used to display a Venn
/// diagram.
/// </summary>
///
/// <remarks>
/// Requirements:
///
/// <para>
/// Excel 2007.
/// </para>
///
/// <para>
/// The NodeXL Excel 2007 Template must be installed, and the version must
/// be 1.0.1.105 or above. This is available at
/// http://nodexl.codeplex.com/Release/ProjectReleases.aspx.
/// </para>
///
/// <para>
/// NodeXL, Graph, Layout must be set to Polar Absolute in the Excel
/// ribbon. NodeXL provided a new sheet to drive this during the
/// period of initial visibility. You must have everything setup
/// properly before setting the worksheet to visible.
/// </para>
///
/// </remarks>
//*************************************************************************
public static void CreateVennDiagramNodeXLFile
(
String filename,
VennDiagramData vdd
)
{
// Create a workbook instance of the NodeXL template
// Populate it iwht the Venn.
// Dev10 errors on the original (next) line. replaced with the line below.
//Application oApplication = new ApplicationClass();
Application oApplication = (Application)Activator.CreateInstance(Type.GetTypeFromProgID("Excel.Application"));
Workbook oWorkbook = CreateNodeXLVennDiagramWorkbook(oApplication, vdd);
oWorkbook.SaveAs(filename, XlFileFormat.xlWorkbookDefault, null, null, false, false, XlSaveAsAccessMode.xlExclusive, null, true, null, null, null);
oApplication.Quit();
}
public VennDiagramData(VennDiagramData vdd)
{
vennType = vdd.vennType;
RegionA = vdd.RegionA;
RegionB = vdd.RegionB;
RegionC = vdd.RegionC;
RegionAB = vdd.RegionAB;
RegionAC = vdd.RegionAC;
RegionBC = vdd.RegionBC;
RegionABC = vdd.RegionABC;
DistanceAB = vdd.DistanceAB;
DistanceAC = vdd.DistanceAC;
DistanceBC = vdd.DistanceBC;
CircleA = new VennCircle(vdd.CircleA);
CircleB = new VennCircle(vdd.CircleB);
if (vennType == VennTypes.ThreeCircle)
{
CircleC = new VennCircle(vdd.CircleC);
}
fScaled = vdd.fScaled;
}
CreateNodeXLVennDiagramWorkbook
(
Application oApplication,
VennDiagramData vdd
)
{
String sTemplatePath;
if (!TryGetTemplatePath(oApplication, out sTemplatePath))
{
OnUnexpectedCondition(Properties.Resources.NodeXLNotInstalled);
}
Workbook oWorkbook = oApplication.Workbooks.Add(sTemplatePath);
// Tell NodeXL to start up in the "Polar Absolute" mode
// and auto display on startup
ListObject oPerWorkbookSettingsTable;
if (!ExcelUtil.TryGetTable(oWorkbook, "Misc", "PerWorkbookSettings",
out oPerWorkbookSettingsTable))
{
OnUnexpectedCondition(Properties.Resources.PerWorkbookTableMissing);
}
SetLayoutAndReadWorkbook(oPerWorkbookSettingsTable);
// The workbook consists of multiple worksheets, but for a Venn diagram
// with no edges, only the vertex worksheet needs to be filled in.
// Get the vertex table on the vertex worksheet.
ListObject oVertexTable;
if (!ExcelUtil.TryGetTable(oWorkbook, "Vertices", "Vertices",
out oVertexTable))
{
OnUnexpectedCondition(Properties.Resources.VertexTableMissing);
}
// make Vertex tab active
Worksheet oWorksheet;
ExcelUtil.TryGetWorksheet(oWorkbook, "Vertices", out oWorksheet);
// See this posting for an explanation of the strange cast:
// http://blogs.officezealot.com/maarten/archive/2006/01/02/8918.aspx
((_Worksheet)oWorksheet).Activate();
AddVennVertices(oVertexTable, vdd);
//AddAlternativeVertexLabels(oVertexTable); // when we need to implement out a different labeling scheme...
return oWorkbook;
}
AddVennVertices
(
ListObject vertexTable,
VennDiagramData vddOriginal
)
{
Debug.Assert(vertexTable != null);
VennDiagramData vdd = vddOriginal.CenterVennDiagramData();
vdd.ScaleTo(150);
// Add two or three vertices. Name them via the Vertex column.
AddVennVertex(vertexTable, vdd.CircleA, 0, "A", "Red");
AddVennVertex(vertexTable, vdd.CircleB, 1, "B", "Green");
if (vdd.vennType == VennDiagramData.VennTypes.ThreeCircle)
{
AddVennVertex(vertexTable, vdd.CircleC, 2, "C", "Blue");
}
}
CreateNodeXLVennDiagramWorkbookFromSequenceRangeGroupings
(
Microsoft.Office.Interop.Excel.Application oApplication,
SequenceRangeGrouping srgA,
SequenceRangeGrouping srgB,
SequenceRangeGrouping srgC
)
{
SequenceRangeGrouping srgOnly_A, srgOnly_B, srgOnly_C, srgOnly_AB, srgOnly_AC, srgOnly_BC, srgOnly_ABC;
CreateSequenceRangeGroupingsForVennDiagram(srgA
, srgB
, srgC
, out srgOnly_A
, out srgOnly_B
, out srgOnly_C
, out srgOnly_AB
, out srgOnly_AC
, out srgOnly_BC
, out srgOnly_ABC);
// generate the intersection Venn metrics
SequenceRangeGroupingMetrics srgmOnly_A = new SequenceRangeGroupingMetrics(srgOnly_A);
SequenceRangeGroupingMetrics srgmOnly_B = new SequenceRangeGroupingMetrics(srgOnly_B);
SequenceRangeGroupingMetrics srgmOnly_C = new SequenceRangeGroupingMetrics(srgOnly_C);
SequenceRangeGroupingMetrics srgmOnly_AB = new SequenceRangeGroupingMetrics(srgOnly_AB);
SequenceRangeGroupingMetrics srgmOnly_AC = new SequenceRangeGroupingMetrics(srgOnly_AC);
SequenceRangeGroupingMetrics srgmOnly_BC = new SequenceRangeGroupingMetrics(srgOnly_BC);
SequenceRangeGroupingMetrics srgmOnly_ABC = new SequenceRangeGroupingMetrics(srgOnly_ABC);
// create the NodeXL Venn diagram filefile
VennDiagramData vdd = new VennDiagramData(srgmOnly_A.bases
, srgmOnly_B.bases
, srgmOnly_C.bases
, srgmOnly_AB.bases
, srgmOnly_AC.bases
, srgmOnly_BC.bases
, srgmOnly_ABC.bases);
// To ensure NodeXL displays the diagram, DONOT make the application
// visible or update the screen until the parameters are all set up.
oApplication.ScreenUpdating = false;
Workbook oWorkbook = CreateNodeXLVennDiagramWorkbook(oApplication, vdd);
// write source data to workbook
DisplaySourceData(srgA, Resources.A, oWorkbook);
DisplaySourceData(srgB, Resources.B, oWorkbook);
DisplaySourceData(srgC, Resources.C, oWorkbook);
// Write overlap data to a sheet
Worksheet outputSheet = oWorkbook.Sheets.Add(Type.Missing, oWorkbook.Sheets[oWorkbook.Sheets.Count], 1, XlSheetType.xlWorksheet);
outputSheet.Name = Resources.OverlapsSheetName;
WriteOverlapData(outputSheet, srgOnly_A, srgOnly_B, srgOnly_C, srgOnly_AB, srgOnly_AC, srgOnly_BC, srgOnly_ABC);
oApplication.ScreenUpdating = true;
oApplication.Visible = true;
return oWorkbook;
}
CreateNodeXLVennDiagramWorkbookFromSequenceRangeGroupings
(
Microsoft.Office.Interop.Excel.Application oApplication,
SequenceRangeGrouping srgA,
SequenceRangeGrouping srgB
)
{
// create the proper sets for VennDiagram
SequenceRangeGrouping srgOnly_A, srgOnly_B, srgOnly_AB;
CreateSequenceRangeGroupingsForVennDiagram(srgA, srgB, out srgOnly_A, out srgOnly_B, out srgOnly_AB);
SequenceRangeGroupingMetrics srgmOnly_A = new SequenceRangeGroupingMetrics(srgOnly_A);
SequenceRangeGroupingMetrics srgmOnly_B = new SequenceRangeGroupingMetrics(srgOnly_B);
SequenceRangeGroupingMetrics srgmOnly_AB = new SequenceRangeGroupingMetrics(srgOnly_AB);
VennDiagramData vdd = new VennDiagramData(srgmOnly_A.bases
, srgmOnly_B.bases
, srgmOnly_AB.bases);
Workbook oWorkbook = CreateNodeXLVennDiagramWorkbook(oApplication, vdd);
// write source data to workbook
DisplaySourceData(srgA, Resources.A, oWorkbook);
DisplaySourceData(srgB, Resources.B, oWorkbook);
// Write overlap data to a sheet
Worksheet outputSheet = oWorkbook.Sheets.Add(Type.Missing, oWorkbook.Sheets[oWorkbook.Sheets.Count], 1, XlSheetType.xlWorksheet);
outputSheet.Name = Resources.OverlapsSheetName;
WriteOverlapData(outputSheet, srgOnly_A, srgOnly_B, srgOnly_AB);
oApplication.Visible = true;
return oWorkbook;
}
public VennDiagramData CenterVennDiagramData()
{
// Shift the circles to be centered about zero
VennDiagramData v = new VennDiagramData(this);
v.Center();
return v;
}
public VennDiagramData(VennDiagramData vdd)
{
vennType = vdd.vennType;
RegionA = vdd.RegionA;
RegionB = vdd.RegionB;
RegionC = vdd.RegionC;
RegionAB = vdd.RegionAB;
RegionAC = vdd.RegionAC;
RegionBC = vdd.RegionBC;
RegionABC = vdd.RegionABC;
DistanceAB = vdd.DistanceAB;
DistanceAC = vdd.DistanceAC;
DistanceBC = vdd.DistanceBC;
CircleA = new VennCircle(vdd.CircleA);
CircleB = new VennCircle(vdd.CircleB);
if (vennType == VennTypes.ThreeCircle)
{
CircleC = new VennCircle(vdd.CircleC);
}
fScaled = vdd.fScaled;
}
public static void Main(string[] args)
{
Splash();
arguments = ProcessCommandLineArguments(args);
VennDiagramData vdd = new VennDiagramData(arguments.regionArray);
if (arguments.polar)
{
vdd.WritePolarVennDiagramData();
}
else
{
vdd.WriteVennDiagramData();
}
if (arguments.xl.Length > 0)
{
// produce an XL file with the 'right stuff'
// Make sure we pass a complete filename path too.
string filename = Path.GetFullPath(arguments.xl);
Console.WriteLine("Produce Excel VennDiagram file: {0}", filename);
VennToNodeXL.CreateVennDiagramNodeXLFile(filename, vdd);
}
}
public static int Main(string[] args)
{
try
{
Splash();
arguments = ProcessCommandLineArguments(args);
if (arguments.inputFiles.Count() == 2)
{
// now read the 2 BED files and do the operation to isolate each set
SequenceRangeGrouping srg1 = ReadBedFile(arguments.inputFiles[0]);
SequenceRangeGrouping srg2 = ReadBedFile(arguments.inputFiles[1]);
SequenceRangeGrouping srgOnly_A, srgOnly_B, srgOnly_AB;
VennToNodeXL.CreateSequenceRangeGroupingsForVennDiagram(
srg1,
srg2,
out srgOnly_A,
out srgOnly_B,
out srgOnly_AB);
var srgmOnly_A = new SequenceRangeGroupingMetrics(srgOnly_A);
var srgmOnly_B = new SequenceRangeGroupingMetrics(srgOnly_B);
var srgmOnly_AB = new SequenceRangeGroupingMetrics(srgOnly_AB);
if (createVennToolInputFile)
{
Console.Error.Write("\nWriting file [{0}]", vennToolInputFileFullPath);
var VennOutput = new StreamWriter(vennToolInputFileFullPath);
VennOutput.WriteLine("{0} {1} {2}", srgmOnly_A.bases, srgmOnly_B.bases, srgmOnly_AB.bases);
VennOutput.Close();
Console.Error.Write(" ... Done.");
}
if (createExcelWorkbook)
{
// create the Excel workbook with a NodeXL Venn diagram
Console.Error.Write("\nWriting file [{0}]", excelWorkbookFullPath);
var vdd = new VennDiagramData(srgmOnly_A.bases, srgmOnly_B.bases, srgmOnly_AB.bases);
try
{
VennToNodeXL.CreateVennDiagramNodeXLFile(excelWorkbookFullPath, vdd);
Console.Error.Write(" ... Done.\n");
}
catch (Exception e)
{
Console.Error.Write("Error: Unable to create Excel workbook.");
DisplayException(e);
Environment.Exit(-1);
}
}
if (verbose)
{
Console.Error.Write("\nDump Sequence Groupings from two files\n");
SequenceRangeGroupingToString(srgOnly_A, "srgOnly_A");
SequenceRangeGroupingToString(srgOnly_B, "srgOnly_B");
SequenceRangeGroupingToString(srgOnly_AB, "srgOnly_AB");
Console.Error.Write("\nEnd Sequence group from twoe files\n");
}
Console.Write("\nOutput basepair count for each set");
Console.Write("\nGroupA,GroupB,GroupAB");
Console.Write("\n{0},{1},{2}\n", srgmOnly_A.bases, srgmOnly_B.bases, srgmOnly_AB.bases);
}
else if (arguments.inputFiles.Count() == 3)
{
// TODO: Reduce memory usage by re-using the SRGs after debugging is complete
//
// now read the 3 BED files and do the operation to isolate each set
SequenceRangeGrouping srg1 = ReadBedFile(arguments.inputFiles[0]);
SequenceRangeGrouping srg2 = ReadBedFile(arguments.inputFiles[1]);
SequenceRangeGrouping srg3 = ReadBedFile(arguments.inputFiles[2]);
SequenceRangeGrouping srgOnly_A,
srgOnly_B,
srgOnly_C,
srgOnly_AB,
srgOnly_AC,
srgOnly_BC,
srgOnly_ABC;
VennToNodeXL.CreateSequenceRangeGroupingsForVennDiagram(
srg1,
srg2,
srg3,
out srgOnly_A,
out srgOnly_B,
out srgOnly_C,
out srgOnly_AB,
out srgOnly_AC,
out srgOnly_BC,
out srgOnly_ABC);
/*
* We have the set information data for the three files.
* Now what?
*/
// generate the intersection Venn metrics
var srgmOnly_A = new SequenceRangeGroupingMetrics(srgOnly_A);
var srgmOnly_B = new SequenceRangeGroupingMetrics(srgOnly_B);
var srgmOnly_C = new SequenceRangeGroupingMetrics(srgOnly_C);
var srgmOnly_AB = new SequenceRangeGroupingMetrics(srgOnly_AB);
var srgmOnly_AC = new SequenceRangeGroupingMetrics(srgOnly_AC);
var srgmOnly_BC = new SequenceRangeGroupingMetrics(srgOnly_BC);
var srgmOnly_ABC = new SequenceRangeGroupingMetrics(srgOnly_ABC);
if (createVennToolInputFile)
{
Console.Error.Write("\nWriting file [{0}]", vennToolInputFileFullPath);
var VennOutput = new StreamWriter(vennToolInputFileFullPath);
VennOutput.WriteLine(
"{0} {1} {2} {3} {4} {5} {6}",
srgmOnly_A.bases,
srgmOnly_B.bases,
srgmOnly_C.bases,
srgmOnly_AB.bases,
srgmOnly_AC.bases,
srgmOnly_BC.bases,
srgmOnly_ABC.bases);
VennOutput.Close();
Console.Error.Write(" ... Done.");
}
if (createExcelWorkbook)
{
// create the NodeXL Venn diagram filefile
var vdd = new VennDiagramData(
srgmOnly_A.bases,
srgmOnly_B.bases,
srgmOnly_C.bases,
srgmOnly_AB.bases,
srgmOnly_AC.bases,
srgmOnly_BC.bases,
srgmOnly_ABC.bases);
// create the Excel workbook with a NodeXL Venn diagram
Console.Error.Write("\nWriting file [{0}]", excelWorkbookFullPath);
try
{
VennToNodeXL.CreateVennDiagramNodeXLFile(excelWorkbookFullPath, vdd);
Console.Error.Write(" ... Done.\n");
}
catch (Exception e)
{
Console.Error.Write("\nError: Unable to create Excel workbook.");
DisplayException(e);
Environment.Exit(-1);
}
}
if (verbose)
{
Console.Error.Write("\nDump Sequence Groupings from three files\n");
SequenceRangeGroupingToString(srgOnly_A, "srgOnly_A");
SequenceRangeGroupingToString(srgOnly_B, "srgOnly_B");
SequenceRangeGroupingToString(srgOnly_C, "srgOnly_C");
SequenceRangeGroupingToString(srgOnly_AB, "srgOnly_AB");
SequenceRangeGroupingToString(srgOnly_AC, "srgOnly_AC");
SequenceRangeGroupingToString(srgOnly_BC, "srgOnly_BC");
SequenceRangeGroupingToString(srgOnly_ABC, "srgOnly_ABC");
Console.Error.Write("\nEnd Sequence group from three files\n");
}
Console.Write("\nOutput basepair count for each set");
Console.Write("\nGroupA,GroupB,GroupC,GroupAB,GroupAC,GroupBC,GroupABC");
Console.Write(
"\n{0},{1},{2},{3},{4},{5},{6}\n",
srgmOnly_A.bases,
srgmOnly_B.bases,
srgmOnly_C.bases,
srgmOnly_AB.bases,
srgmOnly_AC.bases,
srgmOnly_BC.bases,
srgmOnly_ABC.bases);
}
}
catch (Exception ex)
{
DisplayException(ex);
}
return 0;
}
