Are you using Graph Builder? If yes, one can change color by right-clicking the desired variable on the graph legend in JMP11. A script may look something like this:
Names Default To Here( 1 );
dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
graph = dt << Graph Builder(
Show Control Panel( 0 ),
Variables(
X( :age ),
Y( :height ),
Y( :weight, Position( 1 ) ),
Group X( :sex )
),
Elements(
Line(
X,
Y( 1 ),
Y( 2 ),
Legend( 2 ),
Row order( 0 ),
)
),
SendToReport(
Dispatch(
{},
"400",
ScaleBox,
{Legend Model(
2,
Properties( 0, {Line Color( 6 )} ),
Properties( 1, {Line Color( 8 )} )
)}
)
)
);