Reed-CompBio · tristan-f-r · Oct 8, 2025 · Oct 11, 2025 · Oct 11, 2025 · Oct 11, 2025
diff --git a/docs/prms/allpairs.rst b/docs/prms/allpairs.rst
@@ -10,3 +10,21 @@ every single target with respect to a cartesian product.
 All Pairs does not take any arguments. Its source code is at
 https://github.com/Reed-CompBio/all-pairs-shortest-paths licensed under
 MIT.
+
+***************
+ Dataset Usage
+***************
+
+All Pairs Shortest Paths uses ``sources``, ``targets``, and edge
+weights. All Pairs Shortest Paths uses edge direction information.
+However, All Pairs Shortest Paths always returns an undirected
+subnetwork.
+
+************************
+ Implementation Details
+************************
+
+Internally, All Pairs Shortest Paths only accepts fully undirected or
+directed graphs. SPRAS will automatically convert edges to directed
+edges as necessary. For more information, see the section on
+:ref:`algorithm directionality <directionality>`.
diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst
@@ -11,3 +11,19 @@ BowTieBuilder does not take in any arguments.
 
 -  Repository: https://github.com/Reed-CompBio/BowTieBuilder-Algorithm
 -  Paper: https://doi.org/10.1186/1752-0509-3-67
+
+***************
+ Dataset Usage
+***************
+
+BowTieBuilder uses ``sources``, ``targets``, edge weights, and edge
+direction information.
+
+************************
+ Implementation Details
+************************
+
+BowTieBuilder's internal implementation only takes in directed
+interactomes. SPRAS will automatically convert edges to directed edges
+as necessary. For more information, see the section on :ref:`algorithm
+directionality <directionality>`.
diff --git a/docs/prms/domino.rst b/docs/prms/domino.rst
@@ -14,6 +14,14 @@ DOMINO has two optional parameters:
 -  module_threshold: the p-value threshold for considering a putative
    module as final module
 
+***************
+ Dataset Usage
+***************
+
+DOMINO requires the `active` column to be set. DOMINO does not consider
+edge weights, nor graph directionality: directed edges are treated as
+undirected edges, and DOMINO returns an undirected subnetwork.
+
 #################
  Wrapper Details
 #################

diff --git a/docs/prms/meo.rst b/docs/prms/meo.rst
@@ -20,3 +20,19 @@ MEO takes in three optional parameters:
    be true.
 
 -  rand_restarts: the number (int) of random restarts to use.
+
+***************
+ Dataset Usage
+***************
+
+MEO uses ``sources``, ``targets``, and edge weights. MEO also uses edge
+direction information, and the output sub-network is directed.
+
+************************
+ Implementation Details
+************************
+
+Internally, MEO only accepts directed interactomes. SPRAS will
+automatically convert edges to directed edges as necessary. For more
+information, see the section on :ref:`algorithm directionality
+<directionality>`.
diff --git a/docs/prms/mincostflow.rst b/docs/prms/mincostflow.rst
@@ -13,9 +13,24 @@ MinCostFlow takes two optional parameters:
 -  flow: (int) the amount of flow going through the graph
 -  capacity: the (float) max capacity for edges
 
-****************
- External links
-****************
+***************
+ Dataset Usage
+***************
+
+MinCostFlow uses the input's ``sources``, ``targets``, and edge weights.
+MinCostFlow also edge direction information.
+
+************************
+ Implementation Details
+************************
+
+MinCostFlow's internal implementation only accepts directed
+interactomes. SPRAS will automatically convert edges to directed edges
+as necessary. For more information, see the section on :ref:`algorithm
+directionality <directionality>`.
+
+External links
+==============
 
 -  Repository: https://github.com/gitter-lab/min-cost-flow/
 -  MinCostFlow implementation paper:

diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst
@@ -51,3 +51,15 @@ OI1 takes some optional arguments:
       terminal nodes (i.e. nodes without prizes)
    -  ``file``: connect the dummy node to a specific list of nodes
       provided in a file
+
+***************
+ Dataset Usage
+***************
+
+OmicsIntegrator1 prefers ``prize``s, but will take the union of
+``sources`` and ``targets`` and set their 'prize' to 1 if ``prize`` is
+not specified. If any ``dummy_nodes`` are specified, these are passed to
+OmicsIntegrator1 and can have their behavior configured with
+``dummy_mode``.
+
+OmicsIntegrator1 uses edge direction information.
diff --git a/docs/prms/oi2.rst b/docs/prms/oi2.rst
@@ -34,3 +34,14 @@ OI2 takes a few optional arguments:
       -  "all" = connect to all nodes in the interactome.
 
 -  seed: The random seed to use for this run.
+
+***************
+ Dataset Usage
+***************
+
+OmicsIntegrator2 prefers ``prize``s, but will take the union of
+``sources`` and ``targets`` and set their 'prize' to 1 if ``prize`` is
+not specified.
+
+OmicsIntegrator2 does not use edge direction information: all edges are
+treated as undirected, and the output sub-network is undirected.
diff --git a/docs/prms/pathlinker.rst b/docs/prms/pathlinker.rst
@@ -10,9 +10,24 @@ PathLinker takes one optional argument:
 
 -  k: The number of paths to find (*k* shortest paths).
 
-****************
- External links
-****************
+***************
+ Dataset Usage
+***************
+
+PathLinker uses ``sources``, ``targets``, and edge weights. PathLinker
+uses edge direction information.
+
+************************
+ Implementation Details
+************************
+
+Internally, PathLinker only takes in directed graphs. SPRAS will
+automatically convert edges to directed edges as necessary. For more
+information, see the section on :ref:`algorithm directionality
+<directionality>`.
+
+External links
+==============
 
 -  Source code: https://github.com/Murali-group/PathLinker
 -  Associated papers: https://doi.org/10.1038/npjsba.2016.2 and

diff --git a/docs/prms/prms.rst b/docs/prms/prms.rst
@@ -10,6 +10,36 @@
    also supports edge orientation algorithms (e.g. MEO) and active
    module identifiers/disease module mining methods (e.g. DOMINO).
 
+This is the list of SPRAS's supported pathway reconstruction methods.
+Each subpage comes with a description of the algorithm, its source code
+and associated paper (if one exists), and its 'dataset usage,' or parts
+of a dataset that it will utilize when running pathway reconstruction.
+Implementation details are also provided, for users wondering about any
+important decisions that differentiate the SPRAS-wrapped version from
+the original algorithm.
+
+.. _directionality:
+
+************************
+ Directionality Details
+************************
+
+Some algorithms only accept fully undirected or fully directed
+interactomes as input. For input data, SPRAS will try to preserve as
+much directionality information as possible. Mixed interactomes are also
+accepted in SPRAS.
+
+SPRAS will automatically convert the input interactome to the desired
+directionality by the algorithm: this can mean that, for some
+algorithms, interactome direction may be ignored. Other algorithms will
+consider interactome directionality, whether by accepting mixed
+interactomes directly, or converting undirected edges into directed
+edges.
+
+For converting undirected edges to directed edges, unless otherwise
+specified, undirected edges will be converted into two directed edges
+pointing opposite of one another.
+
 .. toctree::
    :maxdepth: 1
    :caption: All Pairs

diff --git a/docs/prms/responsenet.rst b/docs/prms/responsenet.rst
@@ -12,3 +12,19 @@ ResponseNet takes one optional parameter:
 
 -  gamma: (int) controls the size of the output graph: more gamma means
    more 'flow' gets passed along starting from the sources.
+
+***************
+ Dataset Usage
+***************
+
+ResponseNet uses ``sources``, ``targets``, and edge weights. ResponseNet
+uses edge direction information, but returns an undirected subnetwork.
+
+************************
+ Implementation Details
+************************
+
+Internally, ResponseNet only takes in directed graphs. SPRAS will
+automatically convert edges to directed edges as necessary. For more
+information, see the section on :ref:`algorithm directionality
+<directionality>`.
diff --git a/docs/prms/rwr.rst b/docs/prms/rwr.rst
@@ -17,3 +17,23 @@ targets, see STRWR. RWR takes in two parameters:
    restarting.
 
 RWR is implemented at https://github.com/reed-compbio/rwr.
+
+***************
+ Dataset Usage
+***************
+
+RWR considers the union of ``sources`` and ``targets`` as the input
+active nodes. Input interactome directionality is considered, and the
+output subnetwork is also directed.
+
+************************
+ Implementation Details
+************************
+
+RWR returns a ranked list of nodes: SPRAS returns the induced subgraph
+from the number of nodes corresponding to the user-specified
+``threshold``.
+
+Internally, RWR only takes in directed graphs. SPRAS will automatically
+convert edges to directed edges as necessary. For more information, see
+the section on :ref:`algorithm directionality <directionality>`.
diff --git a/docs/prms/strwr.rst b/docs/prms/strwr.rst
@@ -2,9 +2,10 @@
  ST_RWR
 ########
 
-ST_RWR, or random walk with restarts, is a source and target dependent
-pathway reconstruction algorithm that performs PathRank on the input
-interactome, using its edge weights, prizes, sources, and targets.
+ST_RWR, or source-target random walk with restarts, is a source and
+target dependent pathway reconstruction algorithm that performs PathRank
+on the input interactome, using its edge weights, prizes, sources, and
+targets.
 
 For a random walk with restarts implementation that does not use sources
 and targets, see RWR.
@@ -17,3 +18,23 @@ and targets, see RWR.
    restarting.
 
 ST_RWR is implemented at https://github.com/reed-compbio/rwr.
+
+***************
+ Dataset Usage
+***************
+
+ST_RWR considers ``sources`` and ``targets``. ST_RWR considers
+interactome directionality, and the output subnetwork is also directed.
+
+************************
+ Implementation Details
+************************
+
+ST_RWR returns a ranked list of nodes: SPRAS returns the induced
+subgraph from the number of nodes corresponding to the user-specified
+``threshold``.
+
+Internally, ST_RWR only takes in directed graphs. SPRAS will
+automatically convert edges to directed edges as necessary. For more
+information, see the section on :ref:`algorithm directionality
+<directionality>`.