ColorFunction misbehaving for a simple Plot

I’m working through the new data structures in Mathematica 9 and didn’t like the way the missing regions of a TemporalData plot were overlaid in the Documentation,

missingData={2,1,3,Missing[],2,1,2,Missing[],6,2,5};
thirdTemporalData=TemporalData[missingData, Automatic, MissingDataMethod -> Automatic, 
Method->{"Interpolation",InterpolationOrder->3},MetaInformation->{"MissingTimes"->dummy}];
dummy=Flatten[Position[missingData,_Missing]-1];
Show[Plot[thirdTemporalData["PathFunction"][x], {x, 0, 10}],
Table[Plot[thirdTemporalData["PathFunction"][x], {x, i, i + 1},
PlotStyle -> {Thick, Red}],{i, thirdTemporalData["MissingTimes"]}]]

I didn’t like it because when I provided this to Manipulate and switch to the “highlighted” and none “highlighted” plot it changes the graphic size and PlotRange. Also it isn’t as flexible as Id’ like. So I tried the following, but it makes the plot look like I’ve drawn it with a pencil (Imgur: The magic of the Internet in case that image isn’t embedded):

Plot[thirdTemporalData["PathFunction"][t], {t, 0, 10},
PlotRange -> All,ColorFunction->Function[{x, y}, If[3 <= x <= 4 || 7 <= x <= 8, Red,PlotStyle->Automatic]],ColorFunctionScaling->False]


Can anyone explain this and give fix? Thanks.

While the second one is definitely a issue with the ColorFunction rendering (and you may consider contacting Wolfram support) I am not able to reproduce what you mention in the second paragraph. Neither the graphic size nor the range are changed in this formulation:

Manipulate[Show[
  Join[{
    Plot[thirdTemporalData["PathFunction"][x], {x, 0, 
      Length[missingData] - 1}]}, 
   If[highlight, {Table[
      Plot[thirdTemporalData["PathFunction"][x], {x, i - 1, i + 1}, 
       PlotStyle -> {Thick, Red}], {i, 
       thirdTemporalData["MissingTimes"]}]}, {}]]],

{highlight, {False, True}}]

Note, I have modified the range of the second plot to better represent the interpolated segments. Could you please post your own code for this so that we can see what caused you problems?

P.S.: this is a shorter code that pinpoints the issue

Plot[Sin[3 t], {t, 0, 2 Pi}, PlotStyle -> Thickness[.01], 
 ColorFunction -> (If[# < Pi, Red] &), ColorFunctionScaling -> False]
Plot[Sin[3 t], {t, 0, 2 Pi}, PlotStyle -> Thickness[.01]]

Thanks for your reply Giullio. Your implementation of switching between the two plots is much neater than my own - I hadn’t thought to use Join like that!

The plot using ColorFunction has VertexColors in it, and so uses the 3D renderer. As a result, it’s not
getting antialiased, either because the graphic card doesn’t support it, or it’s not turned on in Mathematica
(Preferences > Appearance > Graphics > Antialiasing Quality.)

Here is the screenshot of highest quality setting mentioned by Brett:
Top menu > Edit > Preferences > Appearance > Graphics > Antialiasing Quality