Principal Coordinate/Component Analysis
Data preparation
1) Open excel file “NTSYSclass” in the class folder, it should look like the clip below. You can either input files to NTSYS-pc using Excel or using the application NTedit.
Your loci or OTUs can be
either the columns or the rows, but keep track you have to tell the program
later, which is which. In this case, the OTUs are rows. If you make your
file with Transformer, the OTUs are columns. Also open excel file “dominantsymbol.xls”.
This file specifies populations so when the results are plotted, individuals in
different populations are given different symbols.
Principal Coordinate Analysis
1a) Open Programs-NTSYS-pc21-Ntedit File-Open file in grid.
Browse to the file “NTSYSclass.xls.” This allows you to view the excel file in
the NTS format and it can be saved as a .NTS files if you so choose. Close Ntedit.
1b) Open Programs-NTSYS-pc21-NTSYSpc
2a) Select Similarity left menu
and choose Qualitative Data
2b) Click Help menu in upper right corner of NTSYS window.
Whatever module you are using if you click Help it will open up the relevant
help section.
3) Double click Input File box and browse to ECL290 folder,
change file type to excel. Select “NTSYSclass.xls”
4) Select Rows if your OTUs are rows (they are).
5) Choose J (J = Jaccard’s coefficient) for Coefficient
6) Double click Output file and browse to your eponymous
ECL290 folder. Name Output file “dominant jaccard”, save as type .NTS
(from this point on save all files as type .NTS)
7) Leave Positive (= 1.00000) and Negative (=0.00000)
codes as default
8) Click Compute in top menu bar
The Window you have open should look
like the window on the next page.
Note: Another NTSYS window titled “Report listing” will now open
up and will give you a list of operations you have run and tell you where the
resultant files are saved
8) Select Output and Transf. from the left menu, then click
Dcenter icon
9) Browse to your ECL290 folder and Input matrix file “dominant
jaccard” you will probably have to change the “files of type” to .NTS in order
to see the Jaccard matrix you made and be able to select it.
10) Browse to your ECL290 folder and
name Result matrix “dominant jaccard dcenter”
11a) Leave Square distances box checked
11b) Click Compute
12) Select Ordination from the left menu and then choose
the Eigen module
13) Browse to your ECL290 file and select “dominant jaccard
dcenter” for Input matrix file
14) Browse to your ECL290 file and name Output eigenvector file
“dominant jaccard dcenter vector”
15) Browse to ECL290 file and name Output eigenvalue file “dominant
edit jaccard dcenter value”
16) Leave Number of dimensions as 4 and Sample Size and
Degrees of Freedom as 0
17) Check Show Details Box if you want to see the
operations in the Report Listing box
18) Click Compute
19) Select Graphics from the left menu and then choose Mod3D
plot
20) Browse to ECL290 “your name” folder and choose Input file named
“dominant jaccard dcenter vector”
21) Deselect Plot by rows
22) Browse to ECL290 Ordination file and choose for Plot symbol
input file “dominant symbol” you will have to change file type to all or
.xls to see this file!
23) Leave Graph Matrix File blank
24) Click Compute, you should get a plot that looks
something like that below.
25) In 3D plot window, Plot Options you
can change the size color shape etc of most components of the plot if you want.
The plot can be rotated using the mouse.
