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v2: Drop visualization table (#631)
Remove the visualization table. Let the library handle that. See #629. Closes #629.
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‎doc/v2/documentation_data_format.rst‎

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@@ -78,9 +78,6 @@ format (Figure 2), including:
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- (optional) A simulation file, which has the same format as the measurement
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file, but containing data generated by model simulations [TSV].
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- (optional) A visualization file defining how data and/or simulations should
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be plotted [TSV].
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- (optional) A :ref:`mapping file <v2_mapping_table>` which allows mapping
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PEtab entity IDs to entity IDs in the model, which might not have valid
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PEtab IDs themselves, and to provide additional annotations [TSV].
@@ -162,6 +159,10 @@ PEtab 2.0.0 is a major update of the PEtab format. The main changes are:
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clearer. The ``log10`` transformation has been removed, since this was mostly
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relevant for visualization purposes, and the same effect can be achieved by
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rescaling the parameters of the respective (natural) log-distributions.
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* The visualization table has been removed. The PEtab v1 visualization table
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was not well-defined and not widely used. Visualization is handled by the
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PEtab Python library which also provides documentation on the respective
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input format.
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.. _v2_model:
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.. _v2_model_entities:
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| ... | ... | ... |
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+-----+----------------------------------------------------+----------------------------------------------------+
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Additional (non-standard) columns may be added. If the additional plotting
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functionality of PEtab should be used, such columns could be
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+-----+-------------+---------------+
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| ... | [datasetId] | [replicateId] |
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+=====+=============+===============+
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| ... | [datasetId] | [replicateId] |
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+-----+-------------+---------------+
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| ... | ... | ... |
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+-----+-------------+---------------+
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where ``datasetId`` is a necessary column to use particular plotting
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functionality, and ``replicateId`` is optional, which can be used to group
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replicates and plot error bars.
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Additional (non-standard) columns may be added.
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Detailed field description
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Numeric values or parameter names are allowed. Same rules apply as for
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``observableParameters`` in the previous point.
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- ``datasetId`` [STRING, OPTIONAL]
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The datasetId is used to group certain measurements to datasets. This is
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typically the case for data points which belong to the same observable,
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the same experiment, the same noise model,
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the same observable transformation and the same observable parameters.
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This grouping makes it possible to use the plotting routines that are
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provided by the PEtab Python library.
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- ``replicateId`` [STRING, OPTIONAL]
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The replicateId can be used to discern replicates with the same
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``datasetId``, which is helpful for plotting e.g. error bars.
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.. _v2_observables_table:
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Observables table
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\pi(x|a, b) = \frac{1}{b - a}
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- :math:`[a, b]`
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.. _v2_visualization_table:
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Visualization table
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-------------------
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A tab-separated value file containing the specification of the visualization
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routines which come with the PEtab repository. Plots are in general
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collections of different datasets as specified using their ``datasetId`` (if
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provided) inside the measurement table.
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Expected to have the following columns in any (but preferably this)
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order:
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+--------+------------+-------------------------------------------+------------------------------------------------------+
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| plotId | [plotName] | [plotTypeSimulation] | [plotTypeData] |
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+========+============+===========================================+======================================================+
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| STRING | [STRING] | [LinePlot(default)\|BarPlot\|ScatterPlot] | [MeanAndSD(default)\|MeanAndSEM\|replicate;provided] |
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+--------+------------+-------------------------------------------+------------------------------------------------------+
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| ... | ... | ... | ... |
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+--------+------------+-------------------------------------------+------------------------------------------------------+
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*(wrapped for readability)*
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+-----+-------------+-------------------------------------+-----------+----------+--------------------------+
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| ... | [datasetId] | [xValues] | [xOffset] | [xLabel] | [xScale] |
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+=====+=============+=====================================+===========+==========+==========================+
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| ... | [datasetId] | [time(default)\|parameterOrStateId] | [NUMERIC] | [STRING] | [lin\|log\|log10\|order] |
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+-----+-------------+-------------------------------------+-----------+----------+--------------------------+
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| ... | ... | ... | ... | ... | ... |
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+-----+-------------+-------------------------------------+-----------+----------+--------------------------+
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*(wrapped for readability)*
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+-----+----------------+-----------+----------+-------------------+---------------+
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| ... | [yValues] | [yOffset] | [yLabel] | [yScale] | [legendEntry] |
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+=====+================+===========+==========+===================+===============+
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| ... | [observableId] | [NUMERIC] | [STRING] | [lin\|log\|log10] | [STRING] |
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+-----+----------------+-----------+----------+-------------------+---------------+
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| ... | ... | ... | ... | ... | ... |
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+-----+----------------+-----------+----------+-------------------+---------------+
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Detailed field description
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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- ``plotId`` [STRING, REQUIRED]
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An ID which corresponds to a specific plot. All datasets with the same
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plotId will be plotted into the same axes object.
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- ``plotName`` [STRING, OPTIONAL]
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A name for the specific plot.
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- ``plotTypeSimulation`` [STRING, OPTIONAL]
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The type of the corresponding plot, can be ``LinePlot``, ``BarPlot`` and ``ScatterPlot``. Default is ``LinePlot``.
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- ``plotTypeData`` [STRING, OPTIONAL]
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The type how replicates should be handled, can be ``MeanAndSD``,
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``MeanAndSEM``, ``replicate`` (for plotting all replicates separately), or
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``provided`` (if numeric values for the noise level are provided in the
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measurement table). Default is ``MeanAndSD``.
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- ``datasetId`` [STRING, REFERENCES(measurement.datasetId), OPTIONAL]
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The datasets which should be grouped into one plot.
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- ``xValues`` [STRING, OPTIONAL]
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The independent variable, which will be plotted on the x-axis. Can be
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``time`` (default, for time resolved data), or it can be ``parameterOrStateId``
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for dose-response plots. The corresponding numeric values will be shown on
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the x-axis.
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- ``xOffset`` [NUMERIC, OPTIONAL]
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Possible data-offsets for the independent variable (default is ``0``).
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- ``xLabel`` [STRING, OPTIONAL]
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Label for the x-axis. Defaults to the entry in ``xValues``.
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- ``xScale`` [STRING, OPTIONAL]
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Scale of the independent variable, can be ``lin``, ``log``, ``log10`` or ``order``.
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The ``order`` value should be used if values of the independent variable are
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ordinal. This value can only be used in combination with ``LinePlot`` value for
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the ``plotTypeSimulation`` column. In this case, points on x axis will be
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placed equidistantly from each other. Default is ``lin``.
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- ``yValues`` [observableId, REFERENCES(measurement.observableId), OPTIONAL]
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The observable which should be plotted on the y-axis.
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- ``yOffset`` [NUMERIC, OPTIONAL]
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Possible data-offsets for the observable (default is ``0``).
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- ``yLabel`` [STRING, OPTIONAL]
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Label for the y-axis. Defaults to the entry in ``yValues``.
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- ``yScale`` [STRING, OPTIONAL]
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Scale of the observable, can be ``lin``, ``log``, or ``log10``. Default is ``lin``.
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- ``legendEntry`` [STRING, OPTIONAL]
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The name that should be displayed for the corresponding dataset in the
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legend and which defaults to the value in ``datasetId``.
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Extensions
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~~~~~~~~~~
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Additional columns, such as ``Color``, etc. may be specified. Extensions
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that define operations on multiple PEtab problems need to employ a single
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PEtab YAML file as entrypoint to the analysis. This PEtab file may leave all
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fields specifying files empty and reference the other PEtab problems in the
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extension specific fields.
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Examples
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~~~~~~~~
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Examples of the visualization table can be found in the
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`Benchmark model collection <https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/>`_, for example in the `Chen_MSB2009 <https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/master/Benchmark-Models/Chen_MSB2009>`_
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model.
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.. _v2_mapping_table:
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Mapping table

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