From 6816d3c9f40ed6e4f38d1e6aef5b348104030f13 Mon Sep 17 00:00:00 2001 From: Tristan Figueroa-Reid Date: Wed, 8 Oct 2025 20:51:23 +0000 Subject: [PATCH 1/8] docs: alg usage & impl details --- docs/prms/allpairs.rst | 13 +++++++++++++ docs/prms/bowtiebuilder.rst | 14 ++++++++++++++ docs/prms/domino.rst | 12 ++++++++++++ docs/prms/meo.rst | 6 ++++++ docs/prms/mincostflow.rst | 13 +++++++++++++ docs/prms/oi1.rst | 8 ++++++++ docs/prms/oi2.rst | 9 +++++++++ docs/prms/pathlinker.rst | 15 +++++++++++++++ docs/prms/prms.rst | 6 ++++++ docs/prms/responsenet.rst | 14 ++++++++++++++ docs/prms/rwr.rst | 15 ++++++++++++++- docs/prms/strwr.rst | 15 +++++++++++++-- 12 files changed, 137 insertions(+), 3 deletions(-) diff --git a/docs/prms/allpairs.rst b/docs/prms/allpairs.rst index 1efb7b997..b118b5bcd 100644 --- a/docs/prms/allpairs.rst +++ b/docs/prms/allpairs.rst @@ -8,3 +8,16 @@ 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 also considers graph directionality. + +Implementation Details +---------------------- + +When All Pairs Shortest Paths gets passed a mixed graph, it considers the entire graph to be +directed, by converting all undirected edges to two directed edges pointing +opposite of one another. diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst index c86d59fcf..b02167e05 100644 --- a/docs/prms/bowtiebuilder.rst +++ b/docs/prms/bowtiebuilder.rst @@ -9,3 +9,17 @@ 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``, and edge weights. Input graph +directionality is considered + +Implementation Details +---------------------- + +BowTieBuilder's internal algorithm only takes in directed graphs. +Any pathway inputted into BowTieBuilder gets converted into a directed graph, +where undirected edges get converted into two directed edges pointing opposite of one +another. diff --git a/docs/prms/domino.rst b/docs/prms/domino.rst index a8dac732c..07d4ed90b 100644 --- a/docs/prms/domino.rst +++ b/docs/prms/domino.rst @@ -8,3 +8,15 @@ DOMINO has two optional parameters: * slice_threshold: the p-value threshold for considering a slice as relevant * 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, +but DOMINO does consider graph directionality. + +Implementation Details +---------------------- + +If the input dataframe is empty or too 'small' (where no modules are found), +SPRAS will instead emit an empty output file. diff --git a/docs/prms/meo.rst b/docs/prms/meo.rst index 55157174a..ba3dd29e9 100644 --- a/docs/prms/meo.rst +++ b/docs/prms/meo.rst @@ -12,3 +12,9 @@ MEO takes in three optional parameters: * local_search: a "Yes"/"No" parameter that enables MEO's local search functionality. See "Improving approximations with local search" in the associated paper for more information. This should almost always be yes. * rand_restarts: the number (int) of random restarts to use. + +Dataset Usage +------------- + +MEO uses ``sources``, ``targets``, and edge weights. MEO also considers +input graph directionality. diff --git a/docs/prms/mincostflow.rst b/docs/prms/mincostflow.rst index f519465f9..e1c6eea91 100644 --- a/docs/prms/mincostflow.rst +++ b/docs/prms/mincostflow.rst @@ -11,6 +11,19 @@ MinCostFlow takes two optional parameters: * flow: (int) the amount of flow going through the graph * capacity: the (float) max capacity for edges +Dataset Usage +------------- + +MinCostFlow uses the input's ``sources``, ``targets``, and edge weights. MinCostFlow also +considers directionality. + +Implementation Details +---------------------- + +MinCostFlow converts all undirected edges into directed edges +where undirected edges get converted into two directed edges +pointing opposite of one another. + External links ++++++++++++++ diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst index f5a55db1a..123bbc8be 100644 --- a/docs/prms/oi1.rst +++ b/docs/prms/oi1.rst @@ -24,3 +24,11 @@ OI1 takes some optional arguments: * ``all``: connect the dummy node to all nodes in the interactome (i.e. full set of nodes in graph) * ``others``: connect the dummy node to all nodes that are not 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. + +OmicsIntegrator1 considers graph directionality. diff --git a/docs/prms/oi2.rst b/docs/prms/oi2.rst index f0c5b876b..3f3070947 100644 --- a/docs/prms/oi2.rst +++ b/docs/prms/oi2.rst @@ -18,3 +18,12 @@ OI2 takes a few optional arguments: * "others" = connect to all nodes except for terminals * "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 consider graph directionality. diff --git a/docs/prms/pathlinker.rst b/docs/prms/pathlinker.rst index cb3e045dd..5a767d211 100644 --- a/docs/prms/pathlinker.rst +++ b/docs/prms/pathlinker.rst @@ -10,6 +10,21 @@ PathLinker takes one optional argument: * k: The number of paths to find (*k* shortest paths). +Dataset Usage +------------- + +PathLinker uses ``sources``, ``targets``, and edge weights. PathLinker +considers graph directionality. + +Implementation Details +---------------------- + +PathLinker's internal algorithm only takes in directed graphs. +Any pathway inputted into PathLinker gets converted into a directed graph, +where undirected edges get converted into two directed edges pointing opposite of one +another. + + External links ++++++++++++++ diff --git a/docs/prms/prms.rst b/docs/prms/prms.rst index d661e3d85..f55a702a9 100644 --- a/docs/prms/prms.rst +++ b/docs/prms/prms.rst @@ -6,6 +6,12 @@ Pathway Reconstruction Methods there are other sub-types of algorithms that have more specialized capabilities than the rest. Currently, SPRAS 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 differentriate the SPRAS-wrapped version from the actual +algorithm. + .. toctree:: :maxdepth: 1 :caption: All Pairs diff --git a/docs/prms/responsenet.rst b/docs/prms/responsenet.rst index ec7586d4f..ca5b80112 100644 --- a/docs/prms/responsenet.rst +++ b/docs/prms/responsenet.rst @@ -9,3 +9,17 @@ https://github.com/Reed-CompBio/ResponseNet. 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 +considers graph directionality. + +Implementation Details +---------------------- + +ResponseNet's internal algorithm only takes in directed graphs. +Any pathway inputted into ResponseNet gets converted into a directed graph, +where undirected edges get converted into two directed edges pointing opposite of one +another. diff --git a/docs/prms/rwr.rst b/docs/prms/rwr.rst index b4873332f..d6a12949d 100644 --- a/docs/prms/rwr.rst +++ b/docs/prms/rwr.rst @@ -1,5 +1,5 @@ RWR -========== +=== RWR, or random walk with restarts, is a source and target independent pathway reconstruction algorithm that performs PathRank on the input interactome, using the provided prizes. @@ -11,3 +11,16 @@ RWR takes in two parameters: * alpha: The damping factor of the internal PathRank algorithm. This is the probability that RWR randomly chooses a neighbor instead of 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. + + +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``. diff --git a/docs/prms/strwr.rst b/docs/prms/strwr.rst index 48caa10be..47018d22a 100644 --- a/docs/prms/strwr.rst +++ b/docs/prms/strwr.rst @@ -1,7 +1,7 @@ ST_RWR -========== +====== -ST_RWR, or random walk with restarts, is a source and target dependent pathway reconstruction algorithm +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. @@ -10,3 +10,14 @@ For a random walk with restarts implementation that does not use sources and ta * alpha: The damping factor of the internal PathRank algorithm. This is the probability that RWR randomly chooses a neighbor instead of restarting. ST_RWR is implemented at https://github.com/reed-compbio/rwr. + +Dataset Usage +------------- + +ST_RWR considers ``sources`` and ``targets``. + +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``. From 2984ddbdee9da947c01ef58aec6f75980b67df12 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Fri, 10 Oct 2025 17:02:13 -0700 Subject: [PATCH 2/8] docs: typos Co-authored-by: Anthony Gitter --- docs/prms/prms.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/prms/prms.rst b/docs/prms/prms.rst index f55a702a9..5c4742644 100644 --- a/docs/prms/prms.rst +++ b/docs/prms/prms.rst @@ -9,7 +9,7 @@ Pathway Reconstruction Methods 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 differentriate the SPRAS-wrapped version from the actual +important decisions that differentiate the SPRAS-wrapped version from the original algorithm. .. toctree:: From 87dae00a956fd5cba8a761b1bb6cce8bd320cfd4 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Sat, 11 Oct 2025 00:51:18 +0000 Subject: [PATCH 3/8] docs: update oi1 info --- docs/prms/oi1.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst index 123bbc8be..404a6e405 100644 --- a/docs/prms/oi1.rst +++ b/docs/prms/oi1.rst @@ -29,6 +29,7 @@ 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. +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 considers graph directionality. From c529411fbfa4e221f8f693f0e67d5288ce63f991 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Sun, 19 Oct 2025 14:57:16 -0700 Subject: [PATCH 4/8] docs: punctuation. Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com> --- docs/prms/bowtiebuilder.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst index b02167e05..1838e94fc 100644 --- a/docs/prms/bowtiebuilder.rst +++ b/docs/prms/bowtiebuilder.rst @@ -14,7 +14,7 @@ Dataset Usage ------------- BowTieBuilder uses ``sources``, ``targets``, and edge weights. Input graph -directionality is considered +directionality is considered. Implementation Details ---------------------- From dcb5bea8bced37f479dc8a32a5ad2d306a7ad519 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Mon, 20 Oct 2025 18:22:28 +0000 Subject: [PATCH 5/8] docs: document direction, domino correction --- docs/prms/allpairs.rst | 3 ++- docs/prms/bowtiebuilder.rst | 2 +- docs/prms/domino.rst | 3 ++- docs/prms/meo.rst | 3 ++- docs/prms/oi1.rst | 3 ++- docs/prms/oi2.rst | 3 ++- docs/prms/rwr.rst | 4 ++-- docs/prms/strwr.rst | 3 ++- 8 files changed, 15 insertions(+), 9 deletions(-) diff --git a/docs/prms/allpairs.rst b/docs/prms/allpairs.rst index b118b5bcd..bdb51db73 100644 --- a/docs/prms/allpairs.rst +++ b/docs/prms/allpairs.rst @@ -13,7 +13,8 @@ Dataset Usage ------------- All Pairs Shortest Paths uses ``sources``, ``targets``, and edge weights. -All Pairs Shortest Paths also considers graph directionality. +All Pairs Shortest Paths also can incorporate graph directionality: it accepts directed, undirected, and mixed graphs. +However, All Pairs Shortest Paths always returns an undirected subnetwork. Implementation Details ---------------------- diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst index 1838e94fc..fbed840d7 100644 --- a/docs/prms/bowtiebuilder.rst +++ b/docs/prms/bowtiebuilder.rst @@ -1,5 +1,5 @@ BowTieBuilder -========== +============= BowTieBuilder is a pathway reconstruction algorithm which constructs pathways in a 'bowtie'-like fashion, finding the intersections of shortest paths between sources and targets and using those nodes as a basis diff --git a/docs/prms/domino.rst b/docs/prms/domino.rst index 07d4ed90b..f5365748e 100644 --- a/docs/prms/domino.rst +++ b/docs/prms/domino.rst @@ -13,7 +13,8 @@ Dataset Usage ------------- DOMINO requires the `active` column to be set. DOMINO does not consider edge weights, -but DOMINO does consider graph directionality. +nor graph directionality: directed edges are treated as undirected edges, and DOMINO +returns an undirected subnetwork. Implementation Details ---------------------- diff --git a/docs/prms/meo.rst b/docs/prms/meo.rst index ba3dd29e9..2c280736c 100644 --- a/docs/prms/meo.rst +++ b/docs/prms/meo.rst @@ -17,4 +17,5 @@ Dataset Usage ------------- MEO uses ``sources``, ``targets``, and edge weights. MEO also considers -input graph directionality. +input graph directionality: all undirected edges are converted into directed +edges, and the output sub-network is directed. diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst index 404a6e405..42f138eee 100644 --- a/docs/prms/oi1.rst +++ b/docs/prms/oi1.rst @@ -32,4 +32,5 @@ OmicsIntegrator1 prefers ``prize``s, but will take the union of ``sources`` and 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 considers graph directionality. +OmicsIntegrator1 considers graph directionality: it takes the interactome as is, as it handles graph directionality +internally. diff --git a/docs/prms/oi2.rst b/docs/prms/oi2.rst index 3f3070947..b2bd9c557 100644 --- a/docs/prms/oi2.rst +++ b/docs/prms/oi2.rst @@ -26,4 +26,5 @@ 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 consider graph directionality. +OmicsIntegrator2 does not consider graph directionality: all edges are treated as undirected, +and the output sub-network is undirected. diff --git a/docs/prms/rwr.rst b/docs/prms/rwr.rst index d6a12949d..b1c34a8df 100644 --- a/docs/prms/rwr.rst +++ b/docs/prms/rwr.rst @@ -16,8 +16,8 @@ Dataset Usage ------------- RWR considers the union of ``sources`` and ``targets`` as the -input active nodes. - +input active nodes. The input interactome is treated as directed, and the +output subnetwork is also directed. Implementation Details ---------------------- diff --git a/docs/prms/strwr.rst b/docs/prms/strwr.rst index 47018d22a..4f3dcd979 100644 --- a/docs/prms/strwr.rst +++ b/docs/prms/strwr.rst @@ -14,7 +14,8 @@ ST_RWR is implemented at https://github.com/reed-compbio/rwr. Dataset Usage ------------- -ST_RWR considers ``sources`` and ``targets``. +ST_RWR considers ``sources`` and ``targets``. The input interactome is treated as directed, and the +output subnetwork is also directed. Implementation Details ---------------------- From 15a0b9d0af4996db4726c69d3c5f3ede98987381 Mon Sep 17 00:00:00 2001 From: "Tristan F." Date: Tue, 21 Oct 2025 01:02:53 -0700 Subject: [PATCH 6/8] docs: section on directionality --- docs/prms/allpairs.rst | 8 ++++---- docs/prms/bowtiebuilder.rst | 7 +++---- docs/prms/meo.rst | 10 ++++++++-- docs/prms/mincostflow.rst | 6 +++--- docs/prms/prms.rst | 17 +++++++++++++++++ docs/prms/responsenet.rst | 7 +++---- docs/prms/rwr.rst | 6 +++++- docs/prms/strwr.rst | 8 ++++++-- 8 files changed, 49 insertions(+), 20 deletions(-) diff --git a/docs/prms/allpairs.rst b/docs/prms/allpairs.rst index bdb51db73..8698ff13a 100644 --- a/docs/prms/allpairs.rst +++ b/docs/prms/allpairs.rst @@ -13,12 +13,12 @@ Dataset Usage ------------- All Pairs Shortest Paths uses ``sources``, ``targets``, and edge weights. -All Pairs Shortest Paths also can incorporate graph directionality: it accepts directed, undirected, and mixed graphs. +All Pairs Shortest Paths accepts directed graphs. However, All Pairs Shortest Paths always returns an undirected subnetwork. Implementation Details ---------------------- -When All Pairs Shortest Paths gets passed a mixed graph, it considers the entire graph to be -directed, by converting all undirected edges to two directed edges pointing -opposite of one another. +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 `. diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst index fbed840d7..dcaab99a5 100644 --- a/docs/prms/bowtiebuilder.rst +++ b/docs/prms/bowtiebuilder.rst @@ -19,7 +19,6 @@ directionality is considered. Implementation Details ---------------------- -BowTieBuilder's internal algorithm only takes in directed graphs. -Any pathway inputted into BowTieBuilder gets converted into a directed graph, -where undirected edges get converted into two directed edges pointing opposite of one -another. +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 `. diff --git a/docs/prms/meo.rst b/docs/prms/meo.rst index 2c280736c..8e32bd526 100644 --- a/docs/prms/meo.rst +++ b/docs/prms/meo.rst @@ -17,5 +17,11 @@ Dataset Usage ------------- MEO uses ``sources``, ``targets``, and edge weights. MEO also considers -input graph directionality: all undirected edges are converted into directed -edges, and the output sub-network is directed. +input graph directionality, and the output sub-network is directed. + +Implementation Details +---------------------- + +MEO'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 `. diff --git a/docs/prms/mincostflow.rst b/docs/prms/mincostflow.rst index e1c6eea91..d6899bdfa 100644 --- a/docs/prms/mincostflow.rst +++ b/docs/prms/mincostflow.rst @@ -20,9 +20,9 @@ considers directionality. Implementation Details ---------------------- -MinCostFlow converts all undirected edges into directed edges -where undirected edges get converted into two directed edges -pointing opposite of one another. +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 `. External links ++++++++++++++ diff --git a/docs/prms/prms.rst b/docs/prms/prms.rst index 5c4742644..36f398ebe 100644 --- a/docs/prms/prms.rst +++ b/docs/prms/prms.rst @@ -12,6 +12,23 @@ running pathway reconstruction. Implementation details are also provided, for us 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 index ca5b80112..de482c865 100644 --- a/docs/prms/responsenet.rst +++ b/docs/prms/responsenet.rst @@ -14,12 +14,11 @@ Dataset Usage ------------- ResponseNet uses ``sources``, ``targets``, and edge weights. ResponseNet -considers graph directionality. +considers interactome directionality, but returns an undirected subnetwork. Implementation Details ---------------------- ResponseNet's internal algorithm only takes in directed graphs. -Any pathway inputted into ResponseNet gets converted into a directed graph, -where undirected edges get converted into two directed edges pointing opposite of one -another. +SPRAS will automatically convert edges to directed edges as necessary. +For more information, see the section on :ref:`algorithm directionality `. diff --git a/docs/prms/rwr.rst b/docs/prms/rwr.rst index b1c34a8df..c234917fd 100644 --- a/docs/prms/rwr.rst +++ b/docs/prms/rwr.rst @@ -16,7 +16,7 @@ Dataset Usage ------------- RWR considers the union of ``sources`` and ``targets`` as the -input active nodes. The input interactome is treated as directed, and the +input active nodes. Input interactome directionality is considered, and the output subnetwork is also directed. Implementation Details @@ -24,3 +24,7 @@ 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``. + +RWR's internal algorithm 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 `. diff --git a/docs/prms/strwr.rst b/docs/prms/strwr.rst index 4f3dcd979..8b1cf4edf 100644 --- a/docs/prms/strwr.rst +++ b/docs/prms/strwr.rst @@ -14,11 +14,15 @@ ST_RWR is implemented at https://github.com/reed-compbio/rwr. Dataset Usage ------------- -ST_RWR considers ``sources`` and ``targets``. The input interactome is treated as directed, and the -output subnetwork is also directed. +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``. + +ST_RWR's internal algorithm 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 `. From ab2f8bf5897de4f51cd9f87c7a7e88665e6eb055 Mon Sep 17 00:00:00 2001 From: "Tristan F." Date: Tue, 21 Oct 2025 08:05:00 +0000 Subject: [PATCH 7/8] docs: correct oi1, pathlinker --- docs/prms/oi1.rst | 3 +-- docs/prms/pathlinker.rst | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst index 42f138eee..a975f38ae 100644 --- a/docs/prms/oi1.rst +++ b/docs/prms/oi1.rst @@ -32,5 +32,4 @@ OmicsIntegrator1 prefers ``prize``s, but will take the union of ``sources`` and 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 considers graph directionality: it takes the interactome as is, as it handles graph directionality -internally. +OmicsIntegrator1 accepts mixed directionality graphs. diff --git a/docs/prms/pathlinker.rst b/docs/prms/pathlinker.rst index 5a767d211..051f7aea0 100644 --- a/docs/prms/pathlinker.rst +++ b/docs/prms/pathlinker.rst @@ -20,9 +20,8 @@ Implementation Details ---------------------- PathLinker's internal algorithm only takes in directed graphs. -Any pathway inputted into PathLinker gets converted into a directed graph, -where undirected edges get converted into two directed edges pointing opposite of one -another. +SPRAS will automatically convert edges to directed edges as necessary. +For more information, see the section on :ref:`algorithm directionality `. External links From 21e70333796aa963f688586b7e2fba485c32d18f Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Fri, 24 Oct 2025 12:09:52 -0700 Subject: [PATCH 8/8] docs: update directionality information --- docs/prms/allpairs.rst | 4 ++-- docs/prms/bowtiebuilder.rst | 3 +-- docs/prms/meo.rst | 6 +++--- docs/prms/mincostflow.rst | 2 +- docs/prms/oi1.rst | 2 +- docs/prms/oi2.rst | 2 +- docs/prms/pathlinker.rst | 4 ++-- docs/prms/responsenet.rst | 4 ++-- docs/prms/rwr.rst | 2 +- docs/prms/strwr.rst | 2 +- 10 files changed, 15 insertions(+), 16 deletions(-) diff --git a/docs/prms/allpairs.rst b/docs/prms/allpairs.rst index 8698ff13a..48e173ea7 100644 --- a/docs/prms/allpairs.rst +++ b/docs/prms/allpairs.rst @@ -13,12 +13,12 @@ Dataset Usage ------------- All Pairs Shortest Paths uses ``sources``, ``targets``, and edge weights. -All Pairs Shortest Paths accepts directed graphs. +All Pairs Shortest Paths uses edge direction information. However, All Pairs Shortest Paths always returns an undirected subnetwork. Implementation Details ---------------------- -All Pairs Shortest Paths only accepts fully undirected or directed graphs. +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 `. diff --git a/docs/prms/bowtiebuilder.rst b/docs/prms/bowtiebuilder.rst index dcaab99a5..674d986cb 100644 --- a/docs/prms/bowtiebuilder.rst +++ b/docs/prms/bowtiebuilder.rst @@ -13,8 +13,7 @@ BowTieBuilder does not take in any arguments. Dataset Usage ------------- -BowTieBuilder uses ``sources``, ``targets``, and edge weights. Input graph -directionality is considered. +BowTieBuilder uses ``sources``, ``targets``, edge weights, and edge direction information. Implementation Details ---------------------- diff --git a/docs/prms/meo.rst b/docs/prms/meo.rst index 8e32bd526..6a712cc45 100644 --- a/docs/prms/meo.rst +++ b/docs/prms/meo.rst @@ -16,12 +16,12 @@ MEO takes in three optional parameters: Dataset Usage ------------- -MEO uses ``sources``, ``targets``, and edge weights. MEO also considers -input graph directionality, and the output sub-network is directed. +MEO uses ``sources``, ``targets``, and edge weights. MEO also uses +edge direction information, and the output sub-network is directed. Implementation Details ---------------------- -MEO's internal implementation only accepts directed interactomes. +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 `. diff --git a/docs/prms/mincostflow.rst b/docs/prms/mincostflow.rst index d6899bdfa..f4b7558e2 100644 --- a/docs/prms/mincostflow.rst +++ b/docs/prms/mincostflow.rst @@ -15,7 +15,7 @@ Dataset Usage ------------- MinCostFlow uses the input's ``sources``, ``targets``, and edge weights. MinCostFlow also -considers directionality. +edge direction information. Implementation Details ---------------------- diff --git a/docs/prms/oi1.rst b/docs/prms/oi1.rst index a975f38ae..3380a64a3 100644 --- a/docs/prms/oi1.rst +++ b/docs/prms/oi1.rst @@ -32,4 +32,4 @@ OmicsIntegrator1 prefers ``prize``s, but will take the union of ``sources`` and 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 accepts mixed directionality graphs. +OmicsIntegrator1 uses edge direction information. diff --git a/docs/prms/oi2.rst b/docs/prms/oi2.rst index b2bd9c557..6d034e8ec 100644 --- a/docs/prms/oi2.rst +++ b/docs/prms/oi2.rst @@ -26,5 +26,5 @@ 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 consider graph directionality: all edges are treated as undirected, +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 index 051f7aea0..617ad6490 100644 --- a/docs/prms/pathlinker.rst +++ b/docs/prms/pathlinker.rst @@ -14,12 +14,12 @@ Dataset Usage ------------- PathLinker uses ``sources``, ``targets``, and edge weights. PathLinker -considers graph directionality. +uses edge direction information. Implementation Details ---------------------- -PathLinker's internal algorithm only takes in directed graphs. +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 `. diff --git a/docs/prms/responsenet.rst b/docs/prms/responsenet.rst index de482c865..d6a5f9e3e 100644 --- a/docs/prms/responsenet.rst +++ b/docs/prms/responsenet.rst @@ -14,11 +14,11 @@ Dataset Usage ------------- ResponseNet uses ``sources``, ``targets``, and edge weights. ResponseNet -considers interactome directionality, but returns an undirected subnetwork. +uses edge direction information, but returns an undirected subnetwork. Implementation Details ---------------------- -ResponseNet's internal algorithm only takes in directed graphs. +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 `. diff --git a/docs/prms/rwr.rst b/docs/prms/rwr.rst index c234917fd..f0388380a 100644 --- a/docs/prms/rwr.rst +++ b/docs/prms/rwr.rst @@ -25,6 +25,6 @@ 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``. -RWR's internal algorithm only takes in directed graphs. +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 `. diff --git a/docs/prms/strwr.rst b/docs/prms/strwr.rst index 8b1cf4edf..e0c79a75a 100644 --- a/docs/prms/strwr.rst +++ b/docs/prms/strwr.rst @@ -23,6 +23,6 @@ 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``. -ST_RWR's internal algorithm only takes in directed graphs. +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 `.