教程NTsys主成分分析(PCA)过程.doc
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教程NTsys主成分分析(PCA)过程.doc
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UsingNTSYS-pcforNon-metricMultidimensionalScaling(NMDS)andPrincipalCoordinatesAnalysisofdominantdata
Datapreparation
1)Openexcelfile“dominantedited”intheECL290folder,itshouldlookliketheclipbelow.YoucaneitherinputfilestoNTSYS-pcusingExcelorusingtheapplicationNTedit.
samplebeardataexcel
thereare66rowsand20columns
1
66
20
0
AFLPA1
AFLPA2
AFLPB1
AFLPB2
AFLPC1
pop1Ma1
1
1
1
0
0
pop1Ma2
1
0
1
0
0
pop1Ma3
1
1
1
0
0
pop1Ma4
1
1
1
0
0
pop1Ma5
1
1
0
0
0
pop1Ma6
1
1
1
0
0
pop1Ma7
1
1
1
0
0
pop1Ma8
1
1
1
1
0
YourlociorOTUscanbeeitherthecolumnsortherows,butkeeptrackyouhavetotelltheprogramlater,whichiswhich.Inthiscase,theOTUsarerows.Alsoopenexcelfile“dominantsymbol.xls”(该文件和用于数据分析的.xls有些相同,文件头除了列的位置输入1外,因为只有一列数据,其他相同。
下面部分只有两列:
最左边一列个体名称;第二列是数据,同一群体不同个体数据相同,主要是为了在最后形成的图上对个体做标记。
如图A).Thisfilespecifiespopulationssowhentheresultsareplotted,individualsindifferentpopulationsaregivendifferentsymbols
PrincipalCoordinatesAnalysis
1a)OpenPrograms-NTSYS-pc21-NteditFile-Openfileingrid.BrowsetoG:
driveandchangefiletypetoExcel.ECL290-Datasets-originaldata-ORDINATION-dominant.xlsThisallowsyoutoviewtheexcelfileintheNTSformatanditcanbesavedasa.NTSfilesifyousochoose.CloseNtedit.
1b)OpenPrograms-NTSYS-pc21-NTSYSpc
2a)SelectSimilarityleftmenuandchooseQualitativeData
2b)ClickHelpmenuinupperrightcornerofNTSYSwindow.WhatevermoduleyouareusingmifyouclickHelpitwillopenuptherelevanthelpsection.
3)DoubleclickInputFileboxandbrowsetoECL290folder-Ordination,changefiletypetoexcel.Select“dominant.xls”
4)SelectRowsifyourOTUsarerows(theyare)(本例中标记是在行row,所以要选择。
方框中有×表示选择).
5)ChooseJ(J=Jaccard’scoefficient)forCoefficient
6)DoubleclickOutputfileandbrowsetoyoureponymousECL290folder.NameOutputfile“dominantjaccard”,saveastype.NTS(fromthispointonsaveallfilesastype.NTS)
7)LeavePositive(=1.00000)andNegative(=0.00000)codesasdefault
8)ClickComputeintopmenubar
TheWindowyouhaveopenshouldlooklikethewindowonthenextpage.
Note:
AnotherNTSYSwindowtitled“Reportlisting”willnowopenupandwillgiveyoualistofoperationsyouhaverunandtellyouwheretheresultantfilesaresaved
8)SelectOutputandTransf.fromtheleftmenu,thenclickDcentericon
9)BrowsetoyourECL290folderandInputmatrixfile“dominantjaccard”youwillprobablyhavetochangethe“filesoftype”to.NTSinordertoseetheJaccardmatrixyoumadeandbeabletoselectit.
10)BrowsetoyourECL290folderandnameResultmatrix“dominantjaccarddcenter”
11a)LeaveSquaredistancesboxchecked
11b)ClickCompute
12)SelectOrdinationfromtheleftmenuandthenchoosetheEigenmodule
13)BrowsetoyourECL290fileandselect“dominantjaccarddcenter”forInputmatrixfile
14)BrowsetoyourECL290fileandnameOutputeigenvectorfile“dominantjaccarddcentervector”
15)BrowsetoECL290fileandnameOutputeigenvaluefile“dominanteditjaccarddcentervalue”
16)LeaveNumberofdimensionsas4andSampleSizeandDegreesofFreedomas0
17)CheckShowDetailsBoxifyouwanttoseetheoperationsintheReportListingbox
18)ClickCompute
19)SelectGraphicsfromtheleftmenuandthenchooseMod3Dplot
20)BrowsetoECL290“yourname”folderandchooseInputfilenamed“dominantjaccarddcentervector”
21)DeselectPlotbyrows(此处要取消掉row,点击去掉×)
22)BrowsetoECL290OrdinationfileandchooseforPlotsymbolinputfile“dominantsymbol”youwillhavetochangefiletypetoallor.xlstoseethisfile!
23)LeaveGraphMatrixFileblank
24)ClickCompute,youshouldgetaplotthatlookssomethinglikethatbelow.
25)In3Dplotwindow,PlotOptionsyoucanchangethesizecolorshapeetcofmostcomponentsoftheplotifyouwant.Theplotcanberotatedusingthemouse.
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