Means over Time

Contents

1. The Goal
2. Dummy Data
3. Means Only
4. Make Nice Axes
5. Add Error Bars
6. Make Nice Legend
7. Add Sample Sizes
8. Style Modifications

The Means over Time plot will be developed in several steps. A succinct version of the code is available here.

The Goal

On this page, we walk through the process of creating a means over time graph, complete with error bars and sample sizes. The end goal looks like this:

Dummy Data

The dummy data used to produce this plot was created with the following data step. This data step is only included for the sake of completeness. Do not read, study, or obsess over this data step!

data derive.adlb;
   length paramcd $8 param $100;
   do paramcd = "ALT", "AST";
      if paramcd = "ALT" then 
         param = "Alanine Aminotransferase (IU/L)";
      else if paramcd = "AST" then
         param = "Aspartate Transaminase (IU/L)";
      do trtpn = 1 to 4;
         trtp = 'Treatment ' || put(trtpn,1.);
         do subjid = 1 to 40;
            do avisitn = 0, 1, 2, 4, 6, 8 to 24 by 4;
               length avisit $20;
               if avisitn = 0 then avisit = "B/L";
               else avisit = 'Week ' || strip(put(avisitn,best.));
               aval = 45 + rannor(1)*(1+avisitn/24)*(trtpn/4);
               if ranuni(1) < (50-avisitn)/50 then output;
            end;
         end;
      end;
   end;
run;

Means Only

In this step, we learn how to produce a "means only" plot.

In order to plot means over time, we must first calculate means over time. Fortunately, there's a PROC for that.

proc sort data=derive.adlb out=mot00;
   by trtpn trtp avisitn;
   where paramcd = "ALT";
run;

proc means data=mot00 noprint;
   var aval;
   by trtpn trtp avisitn;
   output out=mot10 n=n mean=mean stderr=stderr;
run;

If we are going to produce a figure for a commercial study, it is probably going to need to be saved as an RTF file. The typical options, ods graphics, and ods rtf statements that surround the sgplot code are as follows:

options 
   nonumber 
   nodate 
   orientation=portrait
   ;

ods graphics / 
   noborder 
   height=6in 
   width=6in
   outputfmt=png
   ;

ods results off;
ods listing close;
ods rtf file="&PgmDir\means_only.rtf";

   <<sgplot portion>>

ods rtf close;
ods listing;
ods results on;

The <<sgplot portion>> contains a series statement along with a couple of basic options.

proc sgplot data=mot10;
   *--- draw the markers and lines ---;
   series y=mean x=avisitn / 
      group=trtpn 
      markers 
      markerattrs=(size=10px)   
      ;
run;

Make Nice Axes

In this step, we make the axes look nice.

First we create a label for the y-axis based on the variable param.

proc sql noprint;
   select   distinct strip(param) || " +/- SE"
   into     :ylabel
   from     mot00
   ;
quit;

%let ylabel = &ylabel;
%put &=ylabel;

The result in the log shows us:

YLABEL=Alanine Aminotransferase (IU/L) +/- SE

Next we create a custom set of tick marks for the x-axis using the variable avisitn.

proc sql noprint;
   select   distinct avisitn
   into     :values separated by " "
   from     mot10
   ;
quit;

%put &=values;

The result in the log shows us:

VALUES=0 1 2 4 6 8 12 16 20 24

We also want to format the value 0 as B/L.

proc format;
   value avisitn
   0 = "B/L"
   other = [best.]
   ;
run;

Finally, we incorporate the above format and macro variables into the plot.

proc sgplot data=mot10;
   *--- draw the markers and lines ---;
   series y=mean x=avisitn / 
      group=trtpn 
      markers markerattrs=(size=10px)       
      ;
   *--- cosmetics ---;
   yaxis
      label="&ylabel"
      ;
   xaxis 
      values=(&values) 
      valuesformat=avisitn.         
      label="Weeks"
      ;
run;

Add Error Bars

Next we add error bars to our plot.

We start by calculating the endpoints of the error bars.

data mot20;
   set mot10;
   upper = mean + stderr;
   lower = mean - stderr;
run;

Then we use the scatter statement to add the error bars to the plot. The parameters yerrorlower and yerrorupper are what cause the bars to be drawn.

proc sgplot data=mot20;
   *--- draw the markers and lines ---;
   series y=mean x=avisitn / 
      group=trtpn 
      markers markerattrs=(size=10px)       
      ;
   *--- draw the error bars ---;
   scatter y=mean x=avisitn /
      group=trtpn 
      yerrorupper=upper 
      yerrorlower=lower
      markerattrs=(size=0px)
      ;
   *--- cosmetics ---;
   yaxis …
   xaxis …
run;

Notice how the error bars at each time point lay on top of one another. This can be remedied by adding the groupdisplay=cluster option to the series and scatter statements.

proc sgplot data=mot20;
   *--- draw the markers and lines ---;
   series y=mean x=avisitn / 
      group=trtpn 
      groupdisplay=cluster
      markers markerattrs=(size=10px)       
      ;
   *--- draw the error bars ---;
   scatter y=mean x=avisitn /
      group=trtpn 
      groupdisplay=cluster
      yerrorupper=upper 
      yerrorlower=lower
      markerattrs=(size=0px)
      ;
   *--- cosmetics ---;
   yaxis …
   xaxis …
run;

Make Nice Legend

Next we clean up the legend.

First we identify all trtpn and trtp combinations, applying the resulting format to the trtpn variables.

proc sql;
   create   table trtp as
   select   distinct "trtp" as fmtname, 
            trtpn as start, 
            trtp as label
   from     mot20
   ;
quit;

proc format cntlin=trtp;
run;

proc sql noprint;
   alter table mot20
      modify trtpn format=trtp.
      ;
quit;

Next we add a keylegend statement. The purpose of options such as title= and noborder are intuitively obvious. The purpose of the text "series" is less obvious. This tells SGPLOT which plot statement the legend should be based off of. You'll notice in the series statement that we have specified name="series", thus allowing us to link it to the keylegend statement.

proc sgplot data=mot20;
   *--- draw the markers and lines ---;
   series y=mean x=avisitn / 
      group=trtpn 
      groupdisplay=cluster          
      markers                       
      markerattrs=(size=10px)       
      name="series"
      ;
   *--- draw the error bars ---;
   scatter …
   *--- cosmetics ---;
   yaxis …
   xaxis …
   keylegend "series" /
      title="Treatment Group"
      noborder
      linelength=15pct
      outerpad=(bottom=10pt)
      ;
run;

Add Sample Sizes

The next-to-last step is to add the sample sizes at each time point.

We use the variable n to create a new variable xatn, complete with a format to prevent missing values to from showing up as a dot.

proc format;
   value xatn
   . = " "
   other = [best.]
   ;
run;

data mot30;
   set mot20;
   if avisitn in (&values) then
      xatn = n;
   format xatn xatn.;
run;

Next we add the xaxistable statement. For some reason SAS has us use the class= option to create groups in the x-axis table (we use the group= option in the series and scatter statements).

proc sgplot data=mot30;
   *--- draw the markers and lines ---;
   series …
   *--- draw the error bars ---;
   scatter …
   *--- add the sample sizes ---;
   xaxistable xatn /
      class=trtpn
      colorgroup=trtpn
      ;
   *--- cosmetics ---;
   yaxis …
   xaxis …
   keylegend …
run;

Style Modifications

As a final step, we perform some style modifications to change colors, symbols, and fonts.

The simplest way to change colors and symbols for grouped data is with the %modstyle macro. Here we use the style rtf to create a new style named motstyle0.

%modstyle
   (name=motstyle0
   ,parent=rtf
   ,type=CLM
   ,colors=black black black black
   ,markers=circle square diamond star
   );

Changing fonts looks a little more awkward. Here we use the motstyle0 from above to create a new style named motstyle. Try not to worry yourself too much about understanding this PROC TEMPLATE code. As long as you understand that Courier New is the font we want in our plot then you've understood enough.

proc template;
   define style styles.motstyle;
      parent=styles.motstyle0;
      class GraphFonts /
         "GraphDataFont"  = ("Courier New, <MTserif>, <serif>", 7pt)
         "GraphValueFont" = ("Courier New, <MTserif>, <serif>", 9pt)
         "GraphLabelFont" = ("Courier New, <MTserif>, <serif>",10pt)
         ;
   end;
run;

Finally, we apply this new style to the ods rtf statement.

ods rtf 
   style=styles.motstyle
   file="&PgmDir\style_mods.rtf"
   ;

proc sgplot data=mot30;
   series …
   scatter …
   xaxistable …
   yaxis…
   xaxis …
   keylegend …
run;

ods rtf close;

And that's all there is to it.

Next page: Kaplan Meier