topic How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file? in SAS Programming

How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Kels123 — Sun, 01 Jul 2018 16:14:27 GMT

Hi,

I need to save my Kaplan-Meier curves in a format other that will be more easily editable for a journal. Right now, SAS is only allowing me to save the images as .png or .bmp files. Is there a way I can just add a outputfmt= statement to my code to output my curves as .ai, .eps, or .pdf files? Here is the code I am using below. Thank you in advance!

data _null_;

%let url = //support.sas.com/documentation/onlinedoc/stat/ex_code/142;

infile "http:&url/templft.html" device=url;

file 'macros.tmp';

retain pre 0;

input;

_infile_ = tranwrd(_infile_, '&', '&');

_infile_ = tranwrd(_infile_, '<' , '<');

if index(_infile_, '</pre>') then pre = 0;

if pre then put _infile_;

if index(_infile_, '<pre>') then pre = 1;

run;

%inc 'macros.tmp' / nosource;

* Modify the template;

%ProvideSurvivalMacros

%let TitleText0 = "Kaplan-Meier Plot: Probability of death, stratified by CD4 count at time of HIV diagnosis";

%let yOptions = label="Survival Probability"

linearopts=(viewmin=0.7 viewmax=1 tickvaluelist=(0.7 0.8 0.9 1.0));

%let xOptions = label="Time (days since release)" ;

%let GraphOpts = DataContrastColors=(green red blue)

DataColors=(green red blue);

/*%let TitleText1 = &titletext0 "CD4 count at diagnosis " STRATUMID;*/

%CompileSurvivalTemplates

*KM stratified by AIDS STAGE**************************************************************;

proc format ;

invalue CD4_atdiagnosiscat '>=500 cells/µL' = 1 '200-499 cells/µL' = 2 '<200 cells/µL' = 3;

value CD4_atdiagnosisfmt 1 = '>=500 cells/µL' 2 = '200-499 cells/µL' 3 = '<200 cells/µL';

run;

data tempCD4(drop=g);

set CLEAN.databasesurv3(rename=(CD4_atdiagnosis=g));

CD4_atdiagnosis = input(g, CD4_atdiagnosiscat.);

run;

* Analysis;

ods graphics on;

proc lifetest data=work.tempCD4 method=km atrisk

plots=(S(test nocensor atrisk(maxlen=16 outside(0.12))=0 to 3000 by 500) /*method=km MAXTIME= 3000 intervals=(0 to 3000 by 500)*/);

time time*EVENT_ANYDEATH(0);

strata CD4_atdiagnosis / order=internal adjust=sidak test=logrank ;

label CD4_atdiagnosis = "CD4 count at diagnosis";

format CD4_atdiagnosis CD4_atdiagnosisfmt.;

run;

ods graphics off;

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

pau13rown — Sun, 01 Jul 2018 16:22:16 GMT

don't journals typically demand tiff?

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Cynthia_sas — Sun, 01 Jul 2018 16:44:12 GMT

Hi, the ODS GRAPHICS statement supports an imagefmt= option. But, the value has to be supported by the destination you're using. I suggest you look at the documentation for the ODS GRAPHICS statement and the imagefmt option.

Cynthia

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Kels123 — Sun, 01 Jul 2018 16:48:20 GMT

Here is what we were instructed: "For any statistical images you should provide editable vector files (ie, the original artwork generated by the statistical package used to make the image); our preferred formats for these files are .ai, .eps, or .pdf." Do you think a .png file would be acceptable based on these guidelines?

I was able to figure out how to generate a pdf file using the bolded statement. However, when looking at the PDF files produced, for some reason SAS is making 2 of the 3 the K-M lines formatted as dotted instead of simple solid lines. This is not how they show up in SAS, which is confusing me and I am not sure how to tweak the code to fix this.

ods graphics on / OUTPUTFMT=pdf imagename="K-M Curve CD4";

ods listing gpath="J:\Kelsey data created 03.16.2016\Kelsey's mortality folder";

proc lifetest data=work.tempCD4 method=km atrisk

plots=(S(test nocensor atrisk(maxlen=16 outside(0.12))=0 to 3000 by 500) /*method=km MAXTIME= 3000 intervals=(0 to 3000 by 500)*/);

time time*EVENT_ANYDEATH(0);

strata CD4_atdiagnosis / order=internal adjust=sidak test=logrank ;

label CD4_atdiagnosis = "CD4 count at diagnosis";

format CD4_atdiagnosis CD4_atdiagnosisfmt.;

run;

ods graphics off;

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

pau13rown — Sun, 01 Jul 2018 20:21:04 GMT

ok, i've been there before. I think i created tiff and then used gimp to convert to eps or pdf. Install gimp 2 then search google 'convert tiff to eps using gimp', something like that

edit: http://gimpchat.com/viewtopic.php?f=8&t=8245

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Reeza — Mon, 02 Jul 2018 04:03:37 GMT

For PDF you can also use ODS PDF.

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Kels123 — Wed, 18 Jul 2018 12:31:34 GMT

I put this code together using outputfmt (also tried imagefmt) but unfortunately PDF is not supported by the destination I am trying to save it to:

ods graphics on / OUTPUTFMT=pdf imagename="K-M Curve CD4";

ods listing gpath="C:\Users\Kelsey\Desktop\SURVIVAL CURVES - PDF ATTEMPTS" ;

proc lifetest data=work.tempCD4 method=km atrisk

plots=(S(test nocensor atrisk (maxlen=16 outside(0.12))=0 to 3000 by 500) /*method=km MAXTIME= 3000 intervals=(0 to 3000 by 500)*/);

time time*EVENT_ANYDEATH(0);

strata CD4_atdiagnosis / order=internal adjust=sidak test=logrank ;

label CD4_atdiagnosis = "CD4 count at diagnosis";

format CD4_atdiagnosis CD4_atdiagnosisfmt.;

run;

ods graphics off;

Any additional suggestions for how to get around this? I find it hard to believe that there is no standardized way of saving a survival curve as a PDF directly from SAS.

Thank you in advance.

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

Cynthia_sas — Wed, 18 Jul 2018 15:14:51 GMT

Hi:

As @Reeza already suggested, you CAN save ALL your output in PDF format by using ODS PDF. For that you don't need imagefmt or outputfmt options.

Cynthia

Re: How do I save a Kaplan-Meier curve as .ai, .eps, or .pdf file?

ChrisHemedinger — Wed, 18 Jul 2018 17:10:42 GMT

You might also want to tweak the resolution for publication -- see tips from @Jay54 on this topic.