:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module


.. _grph_spec:



.. _grph-method_options_spec:

METHOD_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

method options for plt_grph

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: grph


.. _grph-method_options-py_module_spec:

py_module
=========

Type: :term:`one_of(grph) <one_of>`

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: grph


.. _grph-file_paths_spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        output_file_ext: ['svg']
        solutions:
            orig: ./path_to_input_solution.pyml
            final: ./path_to_final_solution.pyml


.. _grph-file_paths-output_folder_spec:

output_folder
=============

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Output folder - results of computation stored here

Example:-

.. code-block:: pyml

    output_folder: auto


.. _grph-file_paths-output_file_ext_spec:

output_file_ext
===============

Type: :term:`list_of(pdf,png,svg) <list_of>`

Output file extension - determines graphical output file format.

Example:-

.. code-block:: pyml

    output_file_ext: ['svg']


.. _grph-file_paths-solutions_spec:

solutions
=========

Type: :term:`dict <dict>`

Solutions to compare

Example:-

.. code-block:: pyml

    solutions:
        orig: ./path_to_input_solution.pyml
        final: ./path_to_final_solution.pyml


.. _grph-data_fields_spec:

DATA_FIELDS
***********

Type: :term:`dict_record <dict_record>`

data fields for popy.dat.fields object

Example:-

.. code-block:: pyml

    DATA_FIELDS:
        type_field: TYPE
        id_field: ID
        time_field: TIME


.. _grph-data_fields-type_field_spec:

type_field
==========

Type: :term:`str <str>`

Field name in data file that contains row type info, e.g. obs/dose etc

Example:-

.. code-block:: pyml

    type_field: TYPE


.. _grph-data_fields-id_field_spec:

id_field
========

Type: :term:`str <str>`

Field name in data file that contains identity string for each data row e.g. obs/dose etc

Example:-

.. code-block:: pyml

    id_field: ID


.. _grph-data_fields-time_field_spec:

time_field
==========

Type: :term:`str <str>`

Field name in data file that contains time or event for each data row

Example:-

.. code-block:: pyml

    time_field: TIME


.. _grph-output_graphs_spec:

OUTPUT_GRAPHS
*************

Type: :term:`list_record <list_record>`

List of graphs to output.

Example:-

.. code-block:: pyml

    OUTPUT_GRAPHS:
        - GRID_SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']
            n_columns: 3

        - COMB_SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']

        - COMB_QUANT_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']
            quantile_list: [0.05, 0.5, 0.95]
            bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
            min_bin_count: 10

        - FE_BAR_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            scaling: prop
            orientation: vertical

        - SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']

        - RE_SPIDER_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            rows_per_page: 1
            columns_per_page: 1
            single_file: False
            scaling: prop
            options_list: []


.. _grph-output_graphs-grid_spag_grph_spec:

GRID_SPAG_GRPH
==============

Type: :term:`dict_record <dict_record>`

Plot data for all individuals on one graph.

Example:-

.. code-block:: pyml

    GRID_SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']
        n_columns: 3


.. _grph-output_graphs-grid_spag_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-grid_spag_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-grid_spag_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-grid_spag_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-grid_spag_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-grid_spag_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-grid_spag_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-grid_spag_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-grid_spag_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-grid_spag_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-grid_spag_grph-x_axis_label_spec:

x_axis_label
------------

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-grid_spag_grph-x_scale_spec:

x_scale
-------

Type: :term:`one_of(linear,log) <one_of>`

x axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    x_scale: linear


.. _grph-output_graphs-grid_spag_grph-y_var_list_spec:

y_var_list
----------

Type: :term:`list(str) <list>`

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']


.. _grph-output_graphs-grid_spag_grph-y_scale_list_spec:

y_scale_list
------------

Type: :term:`list(str) <list>`

List of scales (linear or log) for multiple y axes.

Example:-

.. code-block:: pyml

    y_scale_list: ['linear', 'log']


.. _grph-output_graphs-grid_spag_grph-options_list_spec:

options_list
------------

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-grid_spag_grph-n_columns_spec:

n_columns
---------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    n_columns: 3


.. _grph-output_graphs-comb_spag_grph_spec:

COMB_SPAG_GRPH
==============

Type: :term:`dict_record <dict_record>`

Plot data for all individuals on one graph.

Example:-

.. code-block:: pyml

    COMB_SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-comb_spag_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-comb_spag_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-comb_spag_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-comb_spag_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-comb_spag_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-comb_spag_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-comb_spag_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-comb_spag_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-comb_spag_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-comb_spag_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-comb_spag_grph-x_axis_label_spec:

x_axis_label
------------

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-comb_spag_grph-x_scale_spec:

x_scale
-------

Type: :term:`one_of(linear,log) <one_of>`

x axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    x_scale: linear


.. _grph-output_graphs-comb_spag_grph-y_var_list_spec:

y_var_list
----------

Type: :term:`list(str) <list>`

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']


.. _grph-output_graphs-comb_spag_grph-y_scale_list_spec:

y_scale_list
------------

Type: :term:`list(str) <list>`

List of scales (linear or log) for multiple y axes.

Example:-

.. code-block:: pyml

    y_scale_list: ['linear', 'log']


.. _grph-output_graphs-comb_spag_grph-options_list_spec:

options_list
------------

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-comb_quant_grph_spec:

COMB_QUANT_GRPH
===============

Type: :term:`dict_record <dict_record>`

Plot orig and simulation data using histograms on one graph.

Example:-

.. code-block:: pyml

    COMB_QUANT_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']
        quantile_list: [0.05, 0.5, 0.95]
        bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
        min_bin_count: 10


.. _grph-output_graphs-comb_quant_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-comb_quant_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-comb_quant_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-comb_quant_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-comb_quant_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-comb_quant_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-comb_quant_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-comb_quant_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-comb_quant_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-comb_quant_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-comb_quant_grph-x_axis_label_spec:

x_axis_label
------------

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-comb_quant_grph-x_scale_spec:

x_scale
-------

Type: :term:`one_of(linear,log) <one_of>`

x axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    x_scale: linear


.. _grph-output_graphs-comb_quant_grph-y_var_list_spec:

y_var_list
----------

Type: :term:`list(str) <list>`

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']


.. _grph-output_graphs-comb_quant_grph-y_scale_list_spec:

y_scale_list
------------

Type: :term:`list(str) <list>`

List of scales (linear or log) for multiple y axes.

Example:-

.. code-block:: pyml

    y_scale_list: ['linear', 'log']


.. _grph-output_graphs-comb_quant_grph-options_list_spec:

options_list
------------

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-comb_quant_grph-quantile_list_spec:

quantile_list
-------------

Type: :term:`list(float) <list>`

List of quantiles to plot for each bin of the histogram.

Example:-

.. code-block:: pyml

    quantile_list: [0.05, 0.5, 0.95]


.. _grph-output_graphs-comb_quant_grph-bin_indexer_spec:

bin_indexer
-----------

Type: :term:`one_of_record <one_of_record>`

Possible bin indexing methods.

Example:-

.. code-block:: pyml

    bin_indexer:
        EQUAL_SPACE: {n_bins: auto}


.. _grph-output_graphs-comb_quant_grph-bin_indexer-equal_space_spec:

EQUAL_SPACE
^^^^^^^^^^^

Type: :term:`dict_record <dict_record>`

Equally spaced index builder.

Example:-

.. code-block:: pyml

    EQUAL_SPACE:
        n_bins: auto


.. _grph-output_graphs-comb_quant_grph-bin_indexer-equal_space-n_bins_spec:

n_bins
""""""

Type: :term:`int <int>` / :term:`auto <auto>`

Number of equally spaced bins in index.

Example:-

.. code-block:: pyml

    n_bins: auto


.. _grph-output_graphs-comb_quant_grph-bin_indexer-unequal_space_spec:

UNEQUAL_SPACE
^^^^^^^^^^^^^

Type: :term:`dict_record <dict_record>`

fixed, irregularly spaced user defined bin edges.

Example:-

.. code-block:: pyml

    UNEQUAL_SPACE:
        bin_edge_list: [2.0, 4.0, 8.0]


.. _grph-output_graphs-comb_quant_grph-bin_indexer-unequal_space-bin_edge_list_spec:

bin_edge_list
"""""""""""""

Type: :term:`list(float) <list>`

List of user-defined bin edges.

Example:-

.. code-block:: pyml

    bin_edge_list: [2.0, 4.0, 8.0]


.. _grph-output_graphs-comb_quant_grph-bin_indexer-k_means_spec:

K_MEANS
^^^^^^^

Type: :term:`dict_record <dict_record>`

Deduce bin centres automatically using k-means algorithm for a pre-determined number of bins.

Example:-

.. code-block:: pyml

    K_MEANS:
        n_bins: 10
        init_method: random


.. _grph-output_graphs-comb_quant_grph-bin_indexer-k_means-n_bins_spec:

n_bins
""""""

Type: :term:`int <int>`

Number of bins.

Example:-

.. code-block:: pyml

    n_bins: 10


.. _grph-output_graphs-comb_quant_grph-bin_indexer-k_means-init_method_spec:

init_method
"""""""""""

Type: :term:`one_of(random) <one_of>`

Initialisation method for k-means algorithm.

Example:-

.. code-block:: pyml

    init_method: random


.. _grph-output_graphs-comb_quant_grph-min_bin_count_spec:

min_bin_count
-------------

Type: :term:`int <int>`

Number of data points required to plot an individual bin.

Example:-

.. code-block:: pyml

    min_bin_count: 10


.. _grph-output_graphs-fe_bar_grph_spec:

FE_BAR_GRPH
===========

Type: :term:`dict_record <dict_record>`

Plot bar chart of f[X] values.

Example:-

.. code-block:: pyml

    FE_BAR_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        scaling: prop
        orientation: vertical


.. _grph-output_graphs-fe_bar_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-fe_bar_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-fe_bar_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-fe_bar_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-fe_bar_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-fe_bar_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-fe_bar_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-fe_bar_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-fe_bar_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-fe_bar_grph-scaling_spec:

scaling
-------

Type: :term:`one_of(log,prop) <one_of>`

Scaling with respect to ground truth.

Example:-

.. code-block:: pyml

    scaling: prop


.. _grph-output_graphs-fe_bar_grph-orientation_spec:

orientation
-----------

Type: :term:`one_of(vertical,horizontal) <one_of>`

Orientation of the bars.

Example:-

.. code-block:: pyml

    orientation: vertical


.. _grph-output_graphs-spag_grph_spec:

SPAG_GRPH
=========

Type: :term:`dict_record <dict_record>`

Plot data for each individual.

Example:-

.. code-block:: pyml

    SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-spag_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-spag_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-spag_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-spag_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-spag_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-spag_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-spag_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-spag_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-spag_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-spag_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-spag_grph-x_axis_label_spec:

x_axis_label
------------

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-spag_grph-x_scale_spec:

x_scale
-------

Type: :term:`one_of(linear,log) <one_of>`

x axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    x_scale: linear


.. _grph-output_graphs-spag_grph-y_var_list_spec:

y_var_list
----------

Type: :term:`list(str) <list>`

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']


.. _grph-output_graphs-spag_grph-y_scale_list_spec:

y_scale_list
------------

Type: :term:`list(str) <list>`

List of scales (linear or log) for multiple y axes.

Example:-

.. code-block:: pyml

    y_scale_list: ['linear', 'log']


.. _grph-output_graphs-spag_grph-options_list_spec:

options_list
------------

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy,overlay) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-re_spider_grph_spec:

RE_SPIDER_GRPH
==============

Type: :term:`dict_record <dict_record>`

Plot data on separate graphs for each individual.

Example:-

.. code-block:: pyml

    RE_SPIDER_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        rows_per_page: 1
        columns_per_page: 1
        single_file: False
        scaling: prop
        options_list: []


.. _grph-output_graphs-re_spider_grph-graph_title_spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-re_spider_grph-y_axis_label_list_spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _grph-output_graphs-re_spider_grph-y_var_src_list_spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-re_spider_grph-y_var_label_list_spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-re_spider_grph-y_var_colour_list_spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _grph-output_graphs-re_spider_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

Type: :term:`list(str) <list>`

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-re_spider_grph-rows_per_page_spec:

rows_per_page
-------------

Type: :term:`int <int>`

Number of rows in grid.

Example:-

.. code-block:: pyml

    rows_per_page: 1


.. _grph-output_graphs-re_spider_grph-columns_per_page_spec:

columns_per_page
----------------

Type: :term:`int <int>`

Number of columns in grid.

Example:-

.. code-block:: pyml

    columns_per_page: 1


.. _grph-output_graphs-re_spider_grph-single_file_spec:

single_file
-----------

Type: :term:`bool <bool>`

Render to a single file where possible (PDF only)

Example:-

.. code-block:: pyml

    single_file: False


.. _grph-output_graphs-re_spider_grph-scaling_spec:

scaling
-------

Type: :term:`one_of(log,prop) <one_of>`

Scaling with respect to ground truth.

Example:-

.. code-block:: pyml

    scaling: prop


.. _grph-output_graphs-re_spider_grph-options_list_spec:

options_list
------------

Type: :term:`list_of(overlay) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: []



