From 0503b2f44888b39ab1a9d7af2cc7e5c51b840200 Mon Sep 17 00:00:00 2001 From: 10mubeen Date: Fri, 8 May 2020 13:46:25 +0200 Subject: [PATCH 1/4] fix readme --- README.rst | 52 ++++++++++++++++++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 18 deletions(-) diff --git a/README.rst b/README.rst index 11c4e96..2e0b72d 100644 --- a/README.rst +++ b/README.rst @@ -96,14 +96,16 @@ You can submit your dataset in any of the following formats: - CSV (.csv) - TSV (.tsv) -Please ensure that the dataset has a column 'Node' containing node IDs. If you only provide the node IDs, you can -also include a column in your dataset 'NodeType' indicating the entity type for each node. You can also optionally add -the following columns to your dataset: +Please ensure that the dataset minimally has a column 'Node' containing node IDs. You can also optionally add the +following columns to your dataset: +- NodeType - LogFC [*]_ - p-value -.. [*] log :sub:`2` fold change +.. [*] |Log| fold change + +.. |Log| replace:: Log\ :sub:`2` Input dataset examples ~~~~~~~~~~~~~~~~~~~~~~ @@ -112,8 +114,22 @@ DiffuPath accepts several input formats which can be codified in different ways. `diffusion scores `_ summary for more details. -1. You can provide a dataset with a column 'Node' containing node IDs along with a column 'NodeType' indicating the -entity type. +1. You can provide a dataset with a column 'Node' containing node IDs. + ++------------+ +| Node | ++============+ +| A | ++------------+ +| B | ++------------+ +| C | ++------------+ +| D | ++------------+ + +2. You can also provide a dataset with a column 'Node' containing node IDs as well as a column 'NodeType', indicating +the entity type of the node to run diffusion by entity type. +------------+--------------+ | Node | NodeType | @@ -127,34 +143,34 @@ entity type. | D | Gene | +------------+--------------+ -2. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with -their log :sub:`2` FC. +3. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with +their LogFC. You may also add a 'NodeType' column to run diffusion by entity type. +--------------+------------+ | Node | LogFC | +==============+============+ -| Gene A | 4 | +| A | 4 | +--------------+------------+ -| Gene B | -1 | +| B | -1 | +--------------+------------+ -| Metabolite C | 1.5 | +| C | 1.5 | +--------------+------------+ -| Gene D | 3 | +| D | 3 | +--------------+------------+ -3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their log :sub:`2` -FC and a column 'p-value' with adjusted p-values. +4. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their logFC +and a column 'p-value' with adjusted p-values. You may also add a 'NodeType' column to run diffusion by entity type. +--------------+------------+---------+ | Node | LogFC | p-value | +==============+============+=========+ -| Gene A | 4 | 0.03 | +| A | 4 | 0.03 | +--------------+------------+---------+ -| Gene B | -1 | 0.05 | +| B | -1 | 0.05 | +--------------+------------+---------+ -| Metabolite C | 1.5 | 0.001 | +| C | 1.5 | 0.001 | +--------------+------------+---------+ -| Gene D | 3 | 0.07 | +| D | 3 | 0.07 | +--------------+------------+---------+ You can also take a look at our `sample datasets `_ From fcbabaafabf2fff8b7173ded49821631d973a8e3 Mon Sep 17 00:00:00 2001 From: 10mubeen Date: Fri, 8 May 2020 13:46:46 +0200 Subject: [PATCH 2/4] fix docs --- src/diffupath/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/diffupath/cli.py b/src/diffupath/cli.py index 2193164..795903f 100644 --- a/src/diffupath/cli.py +++ b/src/diffupath/cli.py @@ -79,7 +79,7 @@ def diffusion(): ) @click.option( '-a', '--absolute_value', - help='Codify node labels by applying threshold to |logFC| in input. If absolute_value is set to False, node labels ' + help='Codify node labels by applying threshold to | logFC | in input. If absolute_value is set to False, node labels ' 'will be signed.', type=bool, default=True, From 074b3c515aeec63013fc6c094b5114cabfb7d197 Mon Sep 17 00:00:00 2001 From: 10mubeen Date: Fri, 8 May 2020 13:57:23 +0200 Subject: [PATCH 3/4] update network docs --- docs/source/database.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/database.rst b/docs/source/database.rst index 97b09eb..e797de5 100644 --- a/docs/source/database.rst +++ b/docs/source/database.rst @@ -122,15 +122,15 @@ Custom-network example +-----------+--------------+-------------+ | Source | Target | Relation | +===========+==============+=============+ -| Gene A | Gene B | Increase | +| A | B | Increase | +-----------+--------------+-------------+ -| Gene B | Metabolite C | Association | +| B | C | Association | +-----------+--------------+-------------+ -| Gene A | Pathology D | Association | +| A | D | Association | +-----------+--------------+-------------+ -You can also take a look at our Resources page for some example networks. - +You can also take a look at our `sample networks `_ +folder for some examples networks. References ---------- From 44723bb56d1a7315178efda5be425c97597f2d09 Mon Sep 17 00:00:00 2001 From: 10mubeen Date: Fri, 8 May 2020 14:00:18 +0200 Subject: [PATCH 4/4] update network readme --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index 2e0b72d..0c574dd 100644 --- a/README.rst +++ b/README.rst @@ -300,13 +300,13 @@ Custom-network example ~~~~~~~~~~~~~~~~~~~~~~ +-----------+--------------+-------------+ -| Source | Target | Relation | +| Source | Target | Relation | +===========+==============+=============+ -| Gene A | Gene B | Increase | +| A | B | Increase | +-----------+--------------+-------------+ -| Gene B | Metabolite C | Association | +| B | C | Association | +-----------+--------------+-------------+ -| Gene A | Pathology D | Association | +| A | D | Association | +-----------+--------------+-------------+ You can also take a look at our `sample networks `_