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Datasets (#21)
* update example datasets * fix docs * update sample data * fix docs Co-authored-by: sarah.mubeen <sarah.mubeen@scai.fraunhofer.de>
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‎docs/source/intro.rst‎

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@@ -14,6 +14,7 @@ You can submit your dataset in any of the following formats:
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Please ensure that the dataset minimally has a column 'Node' containing node IDs. You can also optionally add the
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following columns to your dataset:
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- NodeType
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- LogFC [*]_
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- p-value
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| D |
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+------------+
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2. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
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their abs(LogFC).
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2. You can also provide a dataset with a column 'Node' containing node IDs as well as a column 'NodeType', indicating
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the entity type of the node to run diffusion by entity type.
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+------------+--------------+
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| Node | NodeType |
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+============+==============+
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| A | Gene |
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+------------+--------------+
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| B | Gene |
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+------------+--------------+
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| C | Metabolite |
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+------------+--------------+
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| D | Gene |
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+------------+--------------+
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3. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
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their | logFC | . You may also add a 'NodeType' column to run diffusion by entity type.
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+--------------+------------+
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| Node | LogFC |
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+==============+============+
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| Gene A | 4 |
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| A | 4 |
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+--------------+------------+
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| Gene B | -1 |
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| B | -1 |
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+--------------+------------+
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| Metabolite C | 1.5 |
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| C | 1.5 |
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+--------------+------------+
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| Gene D | 3 |
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| D | 3 |
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+--------------+------------+
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3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their abs(LogFC)
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and a column 'p-value' with adjusted p-values.
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.. | logFC | replace:: Log\ :sub:`2`\ FC
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4. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their | logFC |
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and a column 'p-value' with adjusted p-values. You may also add a 'NodeType' column to run diffusion by entity type.
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+--------------+------------+---------+
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| Node | LogFC | p-value |
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+==============+============+=========+
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| Gene A | 4 | 0.03 |
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| A | 4 | 0.03 |
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+--------------+------------+---------+
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| Gene B | -1 | 0.05 |
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| B | -1 | 0.05 |
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+--------------+------------+---------+
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| Metabolite C | 1.5 | 0.001 |
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| C | 1.5 | 0.001 |
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+--------------+------------+---------+
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| Gene D | 3 | 0.07 |
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| D | 3 | 0.07 |
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+--------------+------------+---------+
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You can also take a look at our `sample datasets <https://github.com/multipaths/DiffuPy/tree/master/examples/datasets>`_
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folder for some examples files.
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See the `sample datasets <https://github.com/multipaths/DiffuPy/tree/master/examples/datasets>`_ directory for example
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files.
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Networks
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--------
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~~~~~~~~~~~~~~~~~~~~~~
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+-----------+--------------+-------------+
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| Source | Target | Relation |
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| Source | Target | Relation |
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+===========+==============+=============+
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| Gene A | Gene B | Increase |
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| A | B | Increase |
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+-----------+--------------+-------------+
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| Gene B | Metabolite C | Association |
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| B | C | Association |
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+-----------+--------------+-------------+
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| Gene A | Pathology D | Association |
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| A | D | Association |
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+-----------+--------------+-------------+
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You can also take a look at our `sample networks <https://github.com/multipaths/DiffuPy/tree/master/examples/networks>`_

‎examples/README.rst‎

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Please ensure that the dataset minimally has a column 'Node' containing node IDs. You can also optionally add the
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following columns to your dataset:
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- NodeType
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- LogFC [*]_
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- p-value
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| D |
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+------------+
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2. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
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their | logFC |.
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2. You can also provide a dataset with a column 'Node' containing node IDs as well as a column 'NodeType', indicating
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the entity type of the node to run diffusion by entity type.
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+------------+--------------+
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| Node | NodeType |
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+============+==============+
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| A | Gene |
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+------------+--------------+
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| B | Gene |
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+------------+--------------+
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| C | Metabolite |
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+------------+--------------+
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| D | Gene |
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+------------+--------------+
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3. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
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their | logFC |. You may also add a 'NodeType' column to run diffusion by entity type.
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+--------------+------------+
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| Node | LogFC |
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+==============+============+
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| Gene A | 4 |
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| A | 4 |
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+--------------+------------+
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| Gene B | -1 |
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| B | -1 |
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+--------------+------------+
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| Metabolite C | 1.5 |
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| C | 1.5 |
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+--------------+------------+
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| Gene D | 3 |
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| D | 3 |
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+--------------+------------+
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.. | logFC | replace:: Log\ :sub:`2`\ FC
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3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their | logFC | and
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a column 'p-value' with adjusted p-values.
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4. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their | logFC |
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and a column 'p-value' with adjusted p-values. You may also add a 'NodeType' column to run diffusion by entity type.
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+--------------+------------+---------+
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| Node | LogFC | p-value |
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+==============+============+=========+
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| Gene A | 4 | 0.03 |
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| A | 4 | 0.03 |
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+--------------+------------+---------+
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| Gene B | -1 | 0.05 |
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| B | -1 | 0.05 |
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+--------------+------------+---------+
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| Metabolite C | 1.5 | 0.001 |
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| C | 1.5 | 0.001 |
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+--------------+------------+---------+
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| Gene D | 3 | 0.07 |
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| D | 3 | 0.07 |
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+--------------+------------+---------+
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See the `sample datasets <https://github.com/multipaths/DiffuPy/tree/master/examples/datasets>`_ directory for example
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+-----------+--------------+-------------+
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| Source | Target | Relation |
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+===========+==============+=============+
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| Gene A | Gene B | Increase |
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| A | B | Increase |
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+-----------+--------------+-------------+
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| Gene B | Metabolite C | Association |
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| B | C | Association |
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+-----------+--------------+-------------+
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| Gene A | Pathology D | Association |
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| A | D | Association |
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+-----------+--------------+-------------+
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See the `sample networks <https://github.com/multipaths/DiffuPy/tree/master/examples/networks>`_ directory for some

‎examples/datasets/node_type.csv‎

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Node,NodeType
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A,Gene
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B,Gene
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C,Metabolite
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D,Gene
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E,Metabolite
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F,Gene
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G,Pathology

‎tests/resources/datasets/node_type_col.csv‎

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NodeType,Node
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Gene,A
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Gene,B
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Metabolite,C
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Gene,D
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Gene,E
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Node,NodeType
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A,Gene
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B,Gene
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C,Metabolite
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D,Gene
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E,Metabolite
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F,Gene
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G,Pathology

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