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I have a large data set of experimental data for which I have determined a theoretical fit. However, for some of the experimental data I took, there was systematic error, leading to the data deviating from the expected fit as shown below (experimental values are plotted on x-axis and theoretical values are plotted on y-axis).

graph of data and outliers

Is it possible to write some code to allow one to simply click on the outliers and determine their index, or is there any way to do so natively in Mathematica?

It would also be possible for me to divide the values plotted on the y-axis by those plotted on the x-axis, but I'm wondering whether there's a general method allowing you to click on to identify outliers on any graph.

My code for the graph is as follows (I'm only plotting the first 500 values):

Show[ListPlot[Prepend[Transpose[{experimentalCR[[1 ;; 500]], 
 theoreticalCR[[1 ;; 500]]}], {0, 0}]], ImageSize -> {500, 500}, AspectRatio -> Full]

A sample of the data can be found here:

share|improve this question
@Chris Degnen you're a genius. Thanks a lot! could you specify some references for the method that you have used? – meriens Mar 26 '13 at 10:50
@meriens I'm not sure if Chris will see the comment here. Perhaps you should post it at his answer? – Vincent Tjeng Mar 26 '13 at 13:57
up vote 9 down vote accepted

You might like to try Tooltip:

mixeddata = 
  Prepend[Transpose[{experimentalCR[[1 ;; 500]], 
     theoreticalCR[[1 ;; 500]]}], {0, 0}];

  Tooltip[mixeddata[[i + 1]], i], {i, Length@mixeddata - 1}], 
 ImageSize -> {500, 500}, AspectRatio -> Full]

Or equivalently:

  Tooltip[#1, #2] &, {mixeddata, Range[0, Length@mixeddata - 1]}], 
 ImageSize -> {500, 500}, AspectRatio -> Full]

The graphic is the same, so I won't show it here: the tooltips won't show, after all. The reason I used the index specification that I do is because of that {0,0} you prepreded. If you had added it at the end, this wouldn't have been needed. As kguler's answer shows, you can put anything in the Tooltip.

As another aside, you don't need the Show, you can just apply the desired options (AspectRatio etc) directly in the ListPlot.

As for identifying the outliers, it depends what constitutes outliers in your dataset. For cases like yours with experimental data and theoretical data, here are some suggestions based on styling the individual points. In the each graph, redder dots are greater outliers.

   Style[{##}, Blend[{Red, Black}, (#2/#1)^8]] & @@@ (Rest@mixeddata),
    ImageSize -> 300, AspectRatio -> 1], 
      Hue[1, 1 - (#2/#1)^4, 0.9 - (#2/#1)^8]] & @@@ (Rest@mixeddata), 
   ImageSize -> 300, AspectRatio -> 1]}]

enter image description here

share|improve this answer
thank you for your answer! actually, I prepended the {0,0} because I wanted to force the graph to display the origin - is there any better way to do this? – Vincent Tjeng Feb 26 '13 at 11:24
@VincentTjeng PlotRange -> {{0, 1}, {0, 1}} – Dr. belisarius Feb 26 '13 at 11:35
@belisarius thank you. I'm horrible at searching through documentation. – Vincent Tjeng Feb 26 '13 at 11:38

This method uses single prediction confidence intervals to determine and select outliers. The confidence levels are set to 1, 2 and 3 standard deviations. The points outside 3 SD can be found in o3 and the points outside 1 SD can be found in o1 and o3 combined. The points in o1 and o3 are plotted in the chart in green and red respectively.

data = Transpose@{experimentalCR, theoreticalCR};
{mx, my} = 1.1*Max /@ {experimentalCR, theoreticalCR};

{sd1, sd2, sd3} = 
  2*(CDF[NormalDistribution[0, 1], #] - 0.5) & /@ {1, 2, 3};

lm = LinearModelFit[data, {1, x }, x];

getseries[sd_] := Module[{cb},
  cb = lm["SinglePredictionBands", ConfidenceLevel -> sd];
  {lower, upper} = Transpose[cb /. x -> # & /@ experimentalCR];
  p1 = Position[
    MapThread[#1 <= #2 <= #3 &, {lower, theoreticalCR, upper}], True];
  Extract[data, p1]]

s3 = getseries[sd3];
o3 = Complement[data, s3];

s1 = getseries[sd1];
o1 = Complement[s3, s1];

{bands68[x_], bands95[x_], bands99[x_]} = Table[lm["SinglePredictionBands",
    ConfidenceLevel -> cl], {cl, {sd1, sd2, sd3}}];
 Plot[{lm[x], bands68[x], bands95[x], bands99[x]},
  {x, 0, mx}, Filling -> {2 -> {1}, 3 -> {2}, 4 -> {3}}],
 ListPlot[o1, PlotStyle -> Directive[Green, PointSize[Large]]],
 ListPlot[o3, PlotStyle -> Directive[Red, PointSize[Large]]],
 AxesOrigin -> {0, 0}, PlotRange -> {{0, mx}, {0, my}},
 ImageSize -> 480, Frame -> True]

enter image description here


It seems appropriate to add an alternative method, (although the data in this case does not suggest the suitability of a multivariate fit):-

data = Transpose@{experimentalCR, theoreticalCR};
prange = Sort[#][[{1, -1}]] & /@ {experimentalCR, theoreticalCR};

{{xmin, xmax}, {ymin, ymax}} = {#1, #2*1.35} & @@@ prange;
(* For values within two standard deviations,(approx 95.45% of values) *)
sd = 2;
cl = 2*(CDF[NormalDistribution[0, 1], sd] - 0.5);
e = EllipsoidQuantile[data, cl];
ctr = e[[1]];
{r1, r2} = e[[2]];
inc = ArcTan[e[[3, 1, 2]]/e[[3, 1, 1]]]*180/Pi;
Print["Ellipse center = " <> ToString@ctr];
Print["Ellipse radii (r1, r2) = " <> ToString@{r1, r2}]; Print[
 StringJoin["Ellipse inclination = ", ToString@inc, " degrees"]];

(* Find the foci of the ellipse *)
f = Sqrt[r1^2 - r2^2];
dx = f*Cos[inc Degree];
dy = f*Sin[inc Degree];
f1 = ctr - {dx, dy};
f2 = ctr + {dx, dy};

edge = ctr + r1*e[[3, 1]];
rlim = EuclideanDistance[edge, f1] + EuclideanDistance[edge, f2];
(* nod to belisarius here *)
inside[{x_, y_}, {f1_, f2_}] := 
  Sum[EuclideanDistance[{x, y}, i], {i, {f1, f2}}];
sd = Select[data, inside[#, {f1, f2}] < rlim &];

Show[RegionPlot[inside[{x, y}, {f1, f2}] < rlim,
  {x, xmin, xmax}, {y, ymin, ymax}],
 ListPlot[data], Graphics[{Green, Point@sd}],
 Graphics[{Black, Thick, Dashing[0.05],
   Rotate[Circle[ctr, {r1, r2}], inc Degree]}],
 Graphics[{Red, Line[{ctr + r1*e[[3, 1]], ctr, ctr + r2*e[[3, 2]]}]}],
 Graphics[{Yellow, PointSize[Large], Point[{f1, f2}]}],
 PlotRange -> {{xmin, xmax}, {ymin, ymax}},
 AspectRatio -> (ymax - ymin)/(xmax - xmin), ImageSize -> 300]

enter image description here

share|improve this answer
hi @Chris, what's your reason behind choosing an ellipse here? If i understand correctly, points are considered to be outliers by your program if and only if they lie outside the ellipse. However, assuming that the graph is one of theoretical against experimental values, wouldn't the points have to lie on a line, as in the first part of your explanation? – Vincent Tjeng Mar 2 '13 at 2:18
@Vincent - included it for general reference, (outlier identification). – Chris Degnen Mar 2 '13 at 17:49
I see. thank you! – Vincent Tjeng Mar 3 '13 at 2:03

From a related Q/A: Extracting the coordinate of a particular point of interest from a ListPlot

   data = RandomReal[100, {200, 2}];
   Column[{Row[{"index: ", # }],
    Row[{"values: ", data[[#]]}],
    Row[{"ratio: ", data[[#]][[2]]/data[[#]][[1]]}]}, Center]] & /@
    Range[Length[data]], PlotStyle -> PointSize[Medium]]

enter image description here

Or, replace Tooltip by PopupWindow in the above code to get

enter image description here

share|improve this answer
thank you for the well-explained answer! both you and Verbeia have come up with a great answer that really helps me. However, is there any simple way to click on the data point and add its index to a list which we can extract later? I'm not sure how to extract the index. – Vincent Tjeng Feb 26 '13 at 11:35
@VincentTjeng, please check "Update 2" in the linked Q/A for an example that does something quite similar. – kglr Feb 26 '13 at 11:39
got it, thank you. – Vincent Tjeng Feb 26 '13 at 11:44

Look at my answer here where I use Annotation[...,"Mouse"] and MouseAnnotation[] to get the index of a curve that is clicked on in a plot. The same technique could be applied to individual data points in a LineListPlot[...,Joined->False]. It will not work with ListPlot, which is an older function that does not support Annotation.

share|improve this answer
Thank you, looks like something I should try. – Vincent Tjeng Mar 2 '13 at 2:18

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