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Visualizing Constellation Objects

Collection of functions for generic visualization of information from Constellation Objects.

Visualizing Constellation Objects

    Inspect -- Presents a tabular view of all of the fields stored for a given Constellation object.
    PlotObject -- Provides a visual representation of the information stored in the given Constellation object.
    PlotCloudFile -- Provides an image or preview of an EmeraldCloudFile stored in Constellation.

Plotting Extracted Data from Constellation

    PlotTable -- Given a list of Objects and a list of fields within those objects, generates a table which presents the values of Fields in the provided objects.
    PlotImage -- Given an image file or data objects containing images, provides a visualization of these images that includes a measurement of absolute size scales when possible.
    PlotTableOptions -- Returns all the resolved options for when PlotTable is called on the specified input.

Plotting Data Objects

    PlotELISA -- Displays the absorbance, fluorescence, or analyte concentration vs dilution factors for the supplied ELISA data.
    PlotAbsorbanceKinetics -- Generates a line plot of absorbance intensity as a function of time from the provided absorbance kinetics data.
    PlotAbsorbanceSpectroscopy -- Generates a line plot of the absorbance as a function of wavelength of the provided absorbance spectroscopy data.
    PlotAbsorbanceThermodynamics -- Generates a path plot of absorbance as a function of temperature from melting and cooling curves recorded in the provided absorbance thermodynamics data.
    PlotAgarose -- Generates pixel intensity plots of the agarose gel lane images from the provided AgaroseGelElectrophoresis data.
    PlotAlphaScreen -- Displays the result of an ALPHA screen experiment.
    PlotBioLayerInterferometry -- Generates a line plot of bio-layer thickness as a function of time from the provided bio-layer interferometry (BLI) data.
    PlotCellCount -- Generates an image of the microscope data with the putative cell areas indicated from the provided cell counting image analysis highlighted.
    PlotChromatography -- Generates a line plot of the detector response as a function of time of the provided chromatography data.
    PlotChromatographyMassSpectra -- Generates a waterfall plot showing mass spectra collected from LCMS/GCMS as a function of time. Also provides utilities for generating 2D slices of the 3D (time, m/z, intensity) data.
    PlotCircularDichroism -- Generates a line plot of the circular dichroism (mdeg) as a function of the wavelength (nm) from the provided circular dichroism data objects.
    PlotConductivity -- Generates a column chart of conductivity measurements from the provided conductivity data objects.
    PlotCyclicVoltammetry -- Generates a plot of the raw voltammogram showing the potential difference in millivolts versus the current in microAmperes from the provided cyclic voltammetry data objects.
    PlotCrossFlowFiltration -- Generates plots of all data collected in a cross-flow filtration experimental protocol.
    PlotDifferentialScanningCalorimetry -- Generates a line plot of differential enthalpy as a function of temperature from the provided differential scanning calorimetry (DSC) data.
    PlotDynamicFoamAnalysis -- Generates plots of the foam height, foam volume, bubble count, mean bubble area, average bubble radius and liquid content over time from the provided dynamic foam analysis data objects.
    PlotFluorescenceIntensity -- Generates a histogram or box and whisker plot of the provided fluorescence intensity data.
    PlotFluorescenceKinetics -- Generates a line plot of fluorescent intensity as a function of time from the provided fluorescence kinetics data.
    PlotFluorescenceSpectroscopy -- Generates a line plot of fluorescent intensity as a function of wavelength form the provided fluoresce spectroscopy data.
    PlotFluorescenceThermodynamics -- Generates a path plot of fluorescent intensity as a function of temperature from melting and cooling curves recorded in the provided fluoresce thermodynamics data.
    PlotFreezeCells -- Displays a temperature over time graph obtained from a cell freezing experiment.
    PlotIRSpectroscopy -- Generates a plot of the IR transmittance as a function of wavenumber from the provided infrared spectroscopy data.
    PlotLuminescenceKinetics -- Generates a line plot of luminescence intensity as a function of time from the provided luminescence kinetics data.
    PlotLuminescenceSpectroscopy -- Generates a line plot of relative luminescence as a function of wavelength from the provided luminescence spectroscopy data.
    PlotMassSpectrometry -- Generates a line plot of detector intensity vs mass per charge (m/z) of an ionized particle from the provided mass spectrometry data.
    PlotMicroscope -- Generates an image of the microscope data with frame labels demarking the real-world distances of the items seen in the image in the provided microscope data.
    PlotNephelometry -- Generates a plot of the raw relative nephelometric measurement (RNU) as a function of the concentration of samples in the provided nephelometry data.
    PlotNephelometryKinetics -- Generates a plot of the raw relative nephelometric measurement (RNU) as a function of time of samples in the provided nephelometry kinetics data. A 3D plot can be displayed when dilutions with different concentration of the samples are measured.
    PlotNMR -- Generates a line or waterfall plot of detector intensity as a function of chemical shift with traditionally depicted inverted x-axis for chemical shift of the provided Nuclear Magnetic Resonance (NMR) data.
    PlotNMR2D -- Generates a contour plot of detector intensity as a function of chemical shift of the directly (F2) and indirectly (F1) measured nuclei, with traditionally depicted inverted x-axis for chemical shift of the provided Nuclear Magnetic Resonance (NMR) data.
    PlotPAGE -- Generates an image of the gel lanes side by side with a line plot of the pixel brightness as a function of distance along the lane from the provided Polyacrylamide Gel Electrophoresis (PAGE) data.
    PlotpH -- Generates a column chart of pH measurements from the provided pH data objects.
    PlotPowderXRD -- Generates a line plot of X-ray intensity as a function of diffraction angle from the provided powder X-ray diffraction data.
    PlotqPCR -- Generates a line plot of the normalized fluorescence intensity as a function of replication cycle from the provided qPCR data.
    PlotRamanSpectroscopy -- Generates a line plot of the average Raman spectrum from the provided Raman spectroscopy data, as well as the sampling path and individual Raman spectra for each sampling position.
    PlotSensor -- Generates a line plot of the sensor reading as a function of the date and time from the provided ECL Sensor Array data.
    PlotSurfaceTension -- Generates a list plot of surface tension as a function of concentration from the provided surface tension data.
    PlotTLC -- Displays the result of a thin layer chromatography experiment.
    PlotVacuumEvaporation -- Generates a line plot of pressure and temperature readings as a function of the date and time they were recorded within the evaporation chamber of the speed-vac from the provided vacuum evaporation data.
    PlotVolume -- Generates a histogram or box-and-whisker plot of the distance recorded by ultrasonic sensors in order to determine volume from the provided volume data.
    PlotWestern -- Generates a list plot of the luminescence intensity as a function of molecular weight (as determined from a standard curve relating distance in the gel to molecular weight) from the provided Western data.
    PlotDynamicLightScattering -- Generates a list line plot of intensity vs. particle size from dynamic light scattering data.
    PlotCapillaryIsoelectricFocusing -- Generates a graphical plot of the data stored in a Capillary Isoelectric Focusing data object.
    PlotCapillaryGelElectrophoresisSDS -- Generates a graphical plot of the data stored in Capillary Gel Electrophoresis SDS data.

Plotting Analysis Objects

    PlotAbsorbanceQuantification -- Generates a plot of overlaid absorbance spectroscopy data from replicate reads recorded as part of the given absorbance quantification protocol.
    PlotBindingKinetics -- Generates a plot comparing the prediction of fitted binding kinetics parameters to the source bio-layer interferometry data in the provided binding kinetics analysis object.
    PlotBindingQuantitation -- Generates a plot of the observed binding rate as a function of concentration showing the bio-layer thickness during the quantitation step from the provided BLI analysis object.
    PlotCellCount -- Generates an image of the microscope data with the putative cell areas indicated from the provided cell counting image analysis highlighted.
    PlotCellCountSummary -- Generates an image of the microscope data with the putative cell areas highlighted, along with a pie cart of relative areas of cell groupings from the provided cell counting image analysis highlighted.
    PlotCopyNumber -- Generates a line plot of the fitted standard curve relating quantification cycle (Cq) to Log10[copy number] from the provided copy number analysis object.
    PlotCriticalMicelleConcentration -- Generates a list plot showing the critical micelle concentration above which surface tension is constant from the provided critical micelle concentration analysis object.
    PlotEpitopeBinning -- Generates a graph or table showing the groupings of samples with respect to the interactions with a particular target from a provided BLI experimental protocol.
    PlotFit -- Generates a plot of the source data of a fit overlaid with a line of the fitted equation from a provided fit analysis object.
    PlotFitOptions -- Returns the list of resolved options for when PlotFit is called using the specified input.
    PlotFractions -- Generates a line plot of detector response vs time from source chromatography data with the time slices representing the time for which fractions were collected highlighted from the provided fraction analysis object.
    PlotGating -- Generates a scatter plot off with events colored by their clustering identity from the provided gating analysis object.
    PlotKineticRates -- Generates a line plot of concentration vs time of the predicted kinetic rate fitting from the given kinetic analysis overlaid with the provided source data.
    PlotLadder -- Generates a line plot of the strand length as a function of peak position for standard curve analysis of nucleic acids from the provided ladder analysis object.
    PlotMeltingPoint -- Generates a list plot of the source melting curve analysis along with a demarcation of the fitted melting point.
    PlotMicroscopeOverlay -- Generates a combined false color image of two or more microscope images taken with different filters from the provided microscope overlay analysis object.
    PlotPrediction -- Generates a plot of the source data of a fit overlaid with a line of the fitted equation from a provided fit analysis object along with a line intersecting the fit using the given value and its predicted result via the fit.
    PlotPeaks -- Generates a bar chart or pie chart of the relative peak areas from the provided peak picking analysis object.
    PlotQuantificationCycle -- Generates a list plot of fluorescence intensity as a function of replication cycle with the quantification cycle (Cq) interpolated and highlighted from the provided quantification cycle analysis object.
    PlotSmoothing -- Generates a line plot of smooth data along with the original un-smoothed data points from a provided smoothing analysis object.
    PlotStandardCurve -- Generates a plot of a fitted standard curve overlaid with the data points use to fit it, and the input points the standard was applied to from the provided standard curve analysis object.
    PlotThermodynamics -- Generates a Van't Hoff plot log of Keq as a function of inverse temperature and the fitted line containing the thermodynamic parameters from the provided thermodynamic analysis object.

Plotting Simulation Objects

    PlotProbeConcentration -- Generates a line plot of position vs predicted bound probe concentration from a provided primer set simulation object.
    PlotReactionMechanism -- Generates a graphical representation of a system of nucleic acid reactivity from a provided reaction mechanism.
    PlotState -- Generates a pie chart of relative concentrations of each species in a provided state representation.
    PlotTrajectory -- Generates a line plot of concentration as a function of time from the provided kinetic simulation object or trajectory representation.

Model Plotting

    PlotGlycan -- Generates a graphic of the visual representation corresponding to a commonly accepted abbreviation of the glycan.
    PlotGlycanSequence -- Plots the graphical glycan sequence according to the input.
    PlotProtein -- Generates a 3D ribbon diagram of protein structure diagram from the provided protein model.
    PlotTranscript -- Returns a nucleic acid secondary structure visualization of the provided transcript model.
    PlotVirus -- Returns a electron microscopy image of the virion particle from the provided virus model.

Report Generation

    ExportReport -- Given plots, tables, text or any other data, generates a new notebook page with that information, allowing for automatic report generation.

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