topic Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)? in Graphics Programming

How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 19:27:39 GMT

How can I change the X axis in a CIF plot? It seems to only work for survival plots.

Thanks!

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

Reeza — Thu, 19 Jul 2018 19:32:58 GMT

Code/log?

What version of SAS are you using? I'm assuming you're using PROC PHREG for competing risks?

PS. Replying to a 2years+ thread isn't going to get a response, but it helps if you link to it in your post.

@tbn1 wrote:

How can I change the X axis in a CIF plot? It seems to only work for survival plots.

Thanks!

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 19:40:05 GMT

Hi Reeza,

I am new to this - was trying to respond to your post from 2 years ago. I am using SAS 9.4

I have copied and pasted the response below. I used this code to format my survival curves in proc lifetest and change the axes.

Currently, I am trying to compare and plot competing risks (recurrence) between 2 groups.

Have been using this code:

proc phreg data=bmt plots(overlay=strata)=cif;

class Group / param=glm order=internal ref=first;

model T*Status(0) = Group logWaitTime / eventcode=1;

baseline covariates=risk out=_null_ / rowid=Group;

run;

(from https://support.sas.com/rnd/app/stat/papers/2014/competingrisk2014.pdf)

Thanks!

Formatting from your previous post:

/*SAS PROC LIFETEST Survival Plot Template Modifed by: F. Khurshed Date: July 27, 2011 Description: I modified the basic GTL plot to 1) Changed the thickness of the lines plotted 2) Changed the X axis markers to 12 month intervals 3) Changed the Y axis markers to 0.25 level increments 4) Changed the label of the legend to be a macro variable called legend_label. This needs to be specified prior to output 5) Changed the Y axis markers to be formatted to percent using the tickvalueformat option. (2012-05-01 FK) */

*Template appears in log;
proc template;
define statgraph Stat.Lifetest.Graphics.Productlimitsurvival;
   dynamic NStrata xName plotAtRisk plotCensored plotCL plotHW plotEP labelCL labelHW labelEP maxTime method
      StratumID classAtRisk plotBand plotTest GroupName yMin Transparency SecondTitle TestName pValue;

/*My Macro Variables*/
mvar legend_label;
   BeginGraph;
      if (NSTRATA=1)
         if (EXISTS(STRATUMID))
         entrytitle "Kaplan-Meier " "Survival Estimate" " for " STRATUMID;
      else
         entrytitle "Kaplan-Meier " "Survival Estimate";
      endif;
      if (PLOTATRISK)
         entrytitle "with Number of Subjects at Risk" / textattrs=GRAPHVALUETEXT;
      endif;
      layout overlay / xaxisopts=(shortlabel=XNAME offsetmin=.05 linearopts=(viewmax=MAXTIME /*Modifying X axis values here, need to change below as well*/ tickvaluelist=(0 12 24 36 48 60 72 84 96 108 120))) yaxisopts=(label=
         "Survival Probability" shortlabel="Survival" linearopts=(viewmin=0 viewmax=1 tickvaluelist=(0 .25 .5 .75
         1.0) tickvalueformat=percent8.1 /*Modifying Y axis values here, need to change below as well*/));

/*Add a reference line for the media*/
*referenceline y=0.5/lineattrs=(color=red pattern=2);
         if (PLOTHW=1 AND PLOTEP=0)
            bandplot LimitUpper=HW_UCL LimitLower=HW_LCL x=TIME / modelname="Survival" fillattrs=GRAPHCONFIDENCE
            name="HW" legendlabel=LABELHW;
         endif;
         if (PLOTHW=0 AND PLOTEP=1)
            bandplot LimitUpper=EP_UCL LimitLower=EP_LCL x=TIME / modelname="Survival" fillattrs=GRAPHCONFIDENCE
            name="EP" legendlabel=LABELEP;
         endif;
         if (PLOTHW=1 AND PLOTEP=1)
            bandplot LimitUpper=HW_UCL LimitLower=HW_LCL x=TIME / modelname="Survival" fillattrs=GRAPHDATA1
            datatransparency=.55 name="HW" legendlabel=LABELHW;
         bandplot LimitUpper=EP_UCL LimitLower=EP_LCL x=TIME / modelname="Survival" fillattrs=GRAPHDATA2
            datatransparency=.55 name="EP" legendlabel=LABELEP;
         endif;
         if (PLOTCL=1)
            if (PLOTHW=1 OR PLOTEP=1)
            bandplot LimitUpper=SDF_UCL LimitLower=SDF_LCL x=TIME / modelname="Survival" display=(outline)
            outlineattrs=GRAPHPREDICTIONLIMITS name="CL" legendlabel=LABELCL;
         else
            bandplot LimitUpper=SDF_UCL LimitLower=SDF_LCL x=TIME / modelname="Survival" fillattrs=GRAPHCONFIDENCE
            name="CL" legendlabel=LABELCL;
         endif;
         endif;
         stepplot y=SURVIVAL x=TIME / name="Survival" rolename=(_tip1=ATRISK _tip2=EVENT) tip=(y x Time _tip1
            _tip2) legendlabel="Survival" lineattrs=(thickness=2);
         if (PLOTCENSORED=1)
            scatterplot y=CENSORED x=TIME / markerattrs=(symbol=plus size=8px) name="Censored" legendlabel="Censored";
         endif;
         if (PLOTCL=1 OR PLOTHW=1 OR PLOTEP=1)
            discretelegend "Censored" "CL" "HW" "EP" / location=outside halign=center;
         else
            if (PLOTCENSORED=1)
            discretelegend "Censored" / location=inside autoalign=(topright bottomleft);
         endif;
         endif;
         if (PLOTATRISK=1)
            innermargin / align=bottom;
            blockplot x=TATRISK block=ATRISK / repeatedvalues=true display=(values) valuehalign=start
               valuefitpolicy=truncate labelposition=left labelattrs=GRAPHVALUETEXT valueattrs=GRAPHDATATEXT (size
               =7pt) includemissingclass=false ;
         endinnermargin;
         endif;
      endlayout;
      else
         entrytitle "Kaplan-Meier " "Survival Estimates";
      layout overlay / xaxisopts=(shortlabel=XNAME offsetmin=.05 linearopts=(viewmax=MAXTIME tickvaluelist=(0 12 24 36 48 60 72 84 96 108 120) /*Modifying the X values on graph here, need to change above as well*/)) yaxisopts=(label=
         "Survival Probability" shortlabel="Survival" linearopts=(viewmin=0 viewmax=1 tickvaluelist=(0 .25 .5 .75
         1.0) tickvalueformat=percent8.1 /*Modifying the Y Axis values here, need to change above as well*/));

/*Add a reference line for the media*/
*referenceline y=0.5/lineattrs=(color=red pattern=2);
         if (PLOTHW)
            bandplot LimitUpper=HW_UCL LimitLower=HW_LCL x=TIME / group=STRATUM index=STRATUMNUM modelname=
            "Survival" datatransparency=Transparency;
         endif;
         if (PLOTEP)
            bandplot LimitUpper=EP_UCL LimitLower=EP_LCL x=TIME / group=STRATUM index=STRATUMNUM modelname=
            "Survival" datatransparency=Transparency;
         endif;
         if (PLOTCL)
            if (PLOTBAND)
            bandplot LimitUpper=SDF_UCL LimitLower=SDF_LCL x=TIME / group=STRATUM index=STRATUMNUM modelname=
            "Survival" display=(outline);
         else
            bandplot LimitUpper=SDF_UCL LimitLower=SDF_LCL x=TIME / group=STRATUM index=STRATUMNUM modelname=
            "Survival" datatransparency=Transparency;
         endif;
         endif;
         stepplot y=SURVIVAL x=TIME / group=STRATUM index=STRATUMNUM name="Survival" rolename=(_tip1=ATRISK _tip2=
            EVENT) tip=(y x Time _tip1 _tip2) lineattrs=(thickness=2);
         if (PLOTCENSORED)
            scatterplot y=CENSORED x=TIME / group=STRATUM index=STRATUMNUM markerattrs=(symbol=plus size=8px);
         endif;
         if (PLOTATRISK)
            innermargin / align=bottom;
            blockplot x=TATRISK block=ATRISK / class=STRATUM repeatedvalues=true display=(label values)
               valuehalign=start valuefitpolicy=truncate labelposition=left labelattrs=STRATUMID valueattrs=
               GRAPHDATATEXT (size=7pt) includemissingclass=false;
         endinnermargin;
         endif;
         DiscreteLegend "Survival" / title=legend_label location=outside;
         if (PLOTCENSORED)
            if (PLOTTEST)
            layout gridded / rows=2 autoalign=(TOPRIGHT BOTTOMLEFT TOP BOTTOM) border=false BackgroundColor=
            GraphWalls:Color Opaque=true;
            entry "+ Censored";
            if (PVALUE < .0001)
               entry TESTNAME " p " eval (PUT(PVALUE, PVALUE6.4));
            else
               entry TESTNAME " p=" eval (PUT(PVALUE, PVALUE6.4));
            endif;
         endlayout;
         else
            layout gridded / rows=1 autoalign=(TOPRIGHT BOTTOMLEFT TOP BOTTOM) border=false BackgroundColor=
            GraphWalls:Color Opaque=true;
            entry "+ Censored";
         endlayout;
         endif;
         else
            if (PLOTTEST)
            layout gridded / rows=1 autoalign=(TOPRIGHT BOTTOMLEFT TOP BOTTOM) border=false BackgroundColor=
            GraphWalls:Color Opaque=true;
            if (PVALUE < .0001)
               entry TESTNAME " p " eval (PUT(PVALUE, PVALUE6.4));
            else
               entry TESTNAME " p=" eval (PUT(PVALUE, PVALUE6.4));
            endif;
         endlayout;
         endif;
         endif;
      endlayout;
      endif;
   EndGraph;
end;
run;

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 19:47:31 GMT

Hello, If you want an easy way to make CIF curves and have options to change them I'd suggest trying my macro %NEWSURV. You can find the macro and examples here:

http://www.sascommunity.org/wiki/Kaplan-Meier_Survival_Plotting_Macro_%25NEWSURV

Check out example 6 (and the other examples).

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

Reeza — Thu, 19 Jul 2018 20:08:01 GMT

The code in that post won't work for a CIF plot, you'd need to find a different approach.

Also, since then, SAS has released several macros the control the appearance of survival curves, which is much easier than the solution from a few years ago.

http://documentation.sas.com/?docsetId=statug&docsetTarget=statug_kaplan_toc.htm&docsetVersion=14.3&locale=en

For PROC PHREG, you need to first find the template and then modify it manually.

This walks you through how to first find your template and then how to modify what you need. Note that there's a section of examples as well, but this is generic for any ODS proc.

http://documentation.sas.com/?docsetId=statug&docsetTarget=statug_templt_sect001.htm&docsetVersion=14.3&locale=en

If you're having trouble getting it to work, post back with details of what steps you've take and what is/isn't working.

Also, be careful. You can destroy your template and then it's broken forever, so make sure to save a back up somewhere.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 20:43:55 GMT

Hi Reeza,

Thanks for this information.

Is there a way to reset to the default template for Stat.Phreg.Graphics.CIF if I messed something up?

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

Reeza — Thu, 19 Jul 2018 20:53:12 GMT

Not AFAIK, ergo the recommendation to save a back up copy.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 20:54:18 GMT

Hi Jeff,

I created this:
%macro newsurv(DATA=adj, TIME= Time_After_Surgery__Years__1, CENS=recur, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=0,CLASSORDER=0 1,
COLOR=blue red, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XMAX=5, XINCREMENT=1, XLABEL=Months, YLABEL=Recurrence Risk,

METHOD=CIF, EV_VL=1);
%mend newsurv;

But then do I use proc lifetest plots=cif (Test) to plot this? That did not change anything

%macro newsurv(DATA=adj, TIME= Time_After_Surgery__Years__1, CENS=recur, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=0,CLASSORDER=0 1,
COLOR=blue red, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XMAX=5, XINCREMENT=1, XLABEL=Months, YLABEL=Recurrence Risk,

METHOD=CIF, EV_VL=1);
%mend newsurv;

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 20:55:25 GMT

Thanks - I was playing with your old code before I knew what I was doing and I think I changed it already so I do not have the original template.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

Reeza — Thu, 19 Jul 2018 20:57:34 GMT

That's not the one you need so doesn't affect this question, but will affect future output. I would suggest seeing if a colleague/classmate has not and get it from them. They can change slightly between versions so providing mine wouldn't necessarily solve your issue.

@tbn1 wrote:

Thanks - I was playing with your old code before I knew what I was doing and I think I changed it already so I do not have the original template.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:01:43 GMT

I also wanted to ask if you are aware that the plots created by PHREG are predicted curves and not the actual observed data? LIFETEST will give CIF curves based on the observed data so I would stick with that. If you don't want to try my macro and don't want to keep messing with the template, why not just output the dataset (outCIF) and then do an SGPLOT or write your own template to make the curve you want? Are you trying to make the template have the same changes every time or are you modifying it to make a single graph?

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:04:20 GMT

Hello, The macro itself makes the plot based on a GTL template it makes within the macro.

When you run the macro do not include the %macro and %mend. First run the entire macro code %macro to the %mend from the website, or save it as a program and then %include it.

Then run your macro call like this:

%newsurv(DATA=adj, TIME= Time_After_Surgery__Years__1, CENS=recur, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=0,CLASSORDER=0 1, COLOR=blue red, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XMAX=5, XINCREMENT=1, XLABEL=Months, YLABEL=Recurrence Risk, METHOD=CIF, EV_VL=1);

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:14:47 GMT

I also just saw for CLASSORDER you want to specify the order in a list greater than 1 where the numbers correspond to the alphabetical order of your CLASS variable values. having 0 1 will give an error, so you'd want to do something like CLASSORDER=1 2 or CLASSORDER=2 1.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 21:17:04 GMT

Hi Reeza,

I reset the template to default and changed ONLY the X axis ticks. I was able to change the X axis. However, I am getting these strange lines from the end of the curve (as shown below). This was happening to me before I changed the template too and I was wondering whether you have seen this before? I have pasted template below.

Proc template;
source Stat.Phreg.Graphics.CIF;
define statgraph Stat.PHReg.Graphics.Cif;
   dynamic title1 title2 title3 title4 xviewMin xviewMax group groupIndex groupName plotCL
      transparency _byline_ _bytitle_ _byfootnote_;
   BeginGraph;
      entrytitle TITLE1 TITLE3;
      entrytitle TITLE2 TITLE4 / textattrs=GRAPHVALUETEXT;
      layout overlay / xaxisopts=(linearopts=(viewmin=0 viewmax=5)) yaxisopts=(
         label="Probability");
         if (PLOTCL)
            bandplot LimitLower=LOWERCIF LimitUpper=UPPERCIF x=TIME / group=GROUP index=
               GROUPINDEX modelname="CIF" datatransparency=transparency;
         endif;
         stepplot y=CIF x=TIME / group=GROUP index=GROUPINDEX name="CIF";
         if (EXISTS(GROUP))
            discretelegend "CIF" / location=outside title=GROUPNAME;
         endif;
      endlayout;
      if (_BYTITLE_)
         entrytitle _BYLINE_ / textattrs=GRAPHVALUETEXT;
      else
         if (_BYFOOTNOTE_)
            entryfootnote halign=left _BYLINE_;
         endif;
      endif;
   EndGraph;
end;

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 21:18:05 GMT

Sorry to ask silly questions but I have not done this before. So I run it without my specific data first (with the generic terms on website), then I call it with specifics?

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:21:08 GMT

That is correct. You have to initialize the macro in order to call it later. When you do run your version with your specific parameters you only need to input the ones you are changing, don't worry about running every parameter listed in the macro call. What you posted earlier will be enough to run the macro.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:25:43 GMT

It looks like the data is connecting itself back at 0 for some reason (the last data point is connecting back to the first).

Try changing your stepplot to look like this:

stepplot y=eval(ifn(time<=5,CIF,.)) x=eval(ifn(time <=5,TIME,.)) / group=GROUP index=GROUPINDEX name="CIF";

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 21:28:42 GMT

That does seem like that it is what is happening but that correction made the graph crazier somehow!

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

JeffMeyers — Thu, 19 Jul 2018 21:42:37 GMT

That is strange. How did it become crazier? I don't know what it does behind the scenes as I only know the dataset it makes when the procedure ends.

Re: How to change X axis in CIF plot (either in proc lifetest or proc phreg)?

tbn1 — Thu, 19 Jul 2018 21:45:24 GMT