Bacterial Topography: An Example Workflow

There are many visualization options available with topographical data like the following. You might, for example, be interested in seeing the overall distribution of heights using Histogram:

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cholTop=CloudImport[CloudObject["https://www.wolframcloud.com/obj/online-courses/Published/DataVisualizationWorkflowSample.m"],"ExpressionList"];

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Histogram[Flatten[cholTop]]

Or, with a bit of customization added:

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Histogram[Flatten[cholTop],80,FrameTrue,FrameLabel{"Height [μm]","Count"},FrameStyle14,GridLinesAutomatic,ColorFunction"SolarColors",ChartLegendsPlaced[BarLegend[{"SolarColors",{0,17000}},LegendLabel"Count",LegendLayout"Column",LegendMarkerSize200,LegendFunction(Framed[#,RoundingRadius4,FrameStyleLightGray,BackgroundWhite]&)],{.85,.5}],ImageSize600]

MatrixPlot or ReliefPlot are usually good places to start getting a sense of data like this:

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MatrixPlot[cholTop,PlotLegendsAutomatic]

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ReliefPlot[cholTop,ColorFunction"BlueGreenYellow",PlotLegendsAutomatic,FrameFalse,PerformanceGoal"Quality"]

ListPlot could even be used with Manipulate to get a sense of profile “slices”:

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Manipulate[ListPlot[cholTop[[i]],JoinedTrue],{i,1,Length[cholTop],1}]

You could look in the other direction, too:

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Manipulate[ListPlot[cholTop[[All,i]],JoinedTrue],{i,1,Length[cholTop[[1]]],1}]

Or provide a fancier view:

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Manipulate[ListPlot[cholTop[[i]],JoinedTrue,PlotStyleThickness[.005],PlotRangeMinMax[Flatten[cholTop]],FrameTrue,FrameLabel{"Entry","Height [μm]"},FrameStyle14,GridLinesAutomatic,GridLinesStyleDirective[Gray,Dashed,Opacity[.3]],ColorFunction"BlueGreenYellow",PlotLabel("Slice "<>ToString[i]),ImageSize600],{{i,1,"Slice"},1,Length[cholTop],1}]

Of course, a full 3D view is available via ListPlot3D:

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ListPlot3D[Downsample[cholTop,2],MeshNone,BoxedFalse,AxesFalse,PlotLegendsAutomatic,ColorFunction"BlueGreenYellow",ImageSize600]

By default, ListPlot3D uses box ratios that display the height variation. You could manually rescale to see an “unexaggerated” topography using BoxRatios:

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ListPlot3D[Downsample[cholTop,2],MeshNone,BoxedFalse,AxesFalse,PlotLegendsAutomatic,ColorFunction"BlueGreenYellow",ImageSize600,BoxRatios{1,1,1/350}]