Help with PCA scatter plot confidence ellipses

[Dmonk]

Hello out there,

I need advice on creating a scatter plot of my first two principal componants with confidence ellipses around each of the five species I am investigating, I know how to do this in SAS, but not the enterprise guide.  Here is the input I have been using to get the graph without ellipses:

PROC PRINCOMP DATA=PCA OUT=PCSCORES COVARIANCE;

VAR X1 X2 X3 X4 X5 X6 X7 X8 X9;

title 'PCAVCANMAND';

RUN;

proc gplot DATA=PCSORES;

plot prin2*prin1=Species

RUN;

Any advice on how to add confidence ellipses to the output graph would be appreciated.

[Doc_Duke]

you could just edit the code to look like what you do in regular SAS.

Doc Muhlbaier

Duke

[Dmonk]

...well yes...but what I normally would do in sas is get the output for the PCA, go up to solutions-->analysis-->interactive data analysis, get the PCS scores and then use analyze-->multivariate to get it to produce graphs with ellipses.  Those options don't exist in enterprise but I'm told that it's possible to do.

[Doc_Duke]

Sorry, I can't help further.  I haven't done a PCA in years.    If you are hand coding the entire thing, then PROC SGPLOT might be a good tool to bet your elipses.

[Cynthia_sas]

Hi:

  If you are running SAS 9.2 or higher, you can modify the PRINCOMP code directly to create an ellipse from your PRINCOMP procedure using the PLOTS= option.

  Otherwise, as Doc suggested, if you want to make a dataset and then plot the points yourself, I find SGPLOT to be the most straightforward -- you only need a SCATTER statement and an ELLIPSE statement. Of course, with the PRINCOMP "direct" approach, you only need the PLOTS= option.

  I believe that either one involves modifying the code a bit. The attached program makes some fake data then. shows both approaches.

cynthia

data testdata;

   input grpvar $3. (x1-x14) (1.);

return;

datalines;

s1 26838853879867

s2 74758876857667

s1 56757863775875

s2 67869777988997

s3 99997798878888

s3 89897899888799

s1 89999889899798

s2 87794798468886

s3 35652335143113

s1 89888879576867

s2 76557899446397

s3 97889998898989

s1 76766677598888

s2 99899899899899

s3 76656399567486

;

run;

ods _all_ close;

ods listing close;

ods html path='c:\temp' (url=none)

         file='something.html'  style=egdefault;

ods graphics on;

PROC PRINCOMP DATA=testdata OUT=PCSCORES COVARIANCE

             PLOTS(NCOMP=2)=(SCORE(ellipse));

title '1)PRINCOMP direct approach with ODS GRAPHICS';

VAR X1 X2 X3 X4 X5 X6 X7 X8 X9  ;

RUN;

ods graphics off;

proc sgplot data=pcscores;

  title '2) Use SGPLOT with SCATTER and ELLIPSE';

  scatter x=prin1 y=prin2/group=grpvar;

  ellipse x=prin1 y=prin2;

run;

ods  _all_  close;