update documentation, import fix

bedapub · Dec 7, 2023 · 03202f1 · 03202f1
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diff --git a/README.md b/README.md
@@ -26,9 +26,25 @@ Alexandra Valeanu and Jitao David Zhang with the input and help of many colleagu
 
 Here are few ways to install **kinex**
 
+### From Conda
+
+1. Create and activate your conda environment
+
+```
+	conda create --name kinex
+	conda activate kinex
+```
+
+2. Install kinex package
+
+```
+	conda install -c bioconda kinex
+```
+
+
 ### From source
 
-1. Create and activate a python 3.11 conda venv:
+1. Create and activate a python 3.11 conda environment 
 
 ```
 conda create --name kinex

diff --git a/docs/chapters/features/comparison.rst b/docs/chapters/features/comparison.rst
@@ -17,7 +17,7 @@ Drug comparison
 Compare multiple experiments with each other
 --------------------------------------------
 
-3. Specify the path to the tables
+3. Specify the path to your enrichment tables
 
 .. code:: python
 
@@ -26,7 +26,7 @@ Compare multiple experiments with each other
 
 .. note:: 
 
-    The directory should have multiple ``.csv`` files that contain enrichment analysis results from kinex
+    The directory should have multiple ``.csv`` files that contain enrichment analysis result tables from kinex
 
     .. code::
 
@@ -56,14 +56,19 @@ Compare multiple experiments with each other
     :file: ../../figures/comparison_multiple_drugs.html
 
 
-6. You can optionally :ref:`save the plot in a desired format<Save the plot in a desired format>`
+.. note::
 
+    You can update your figure (marker point, axis, legend, etc.) using Plotly’s functions:
+    `https://plotly.com/python/creating-and-updating-figures <https://plotly.com/python/creating-and-updating-figures>`_
 
-Compare an experiment to the one existing database of drugs
------------------------------------------------------------
 
-3. Read the table with enrichment analysis results
+6. You can optionally :ref:`save the plot in a desired format<Save the plot in a desired format>`
+
 
+Compare an experiment to the existing collection of drug profiles
+-----------------------------------------------------------------
+
+3. Read the enrichment analysis result table
 
 .. code:: python
 
@@ -98,7 +103,7 @@ Compare an experiment to the one existing database of drugs
 
 .. note:: 
 
-    Supported methods are UMAP, MDS and t-SNE
+    Supported methods are ``UMAP``, ``MDS``, and ``t-SNE``
 
 
 5. Show the graph
@@ -119,8 +124,6 @@ Compare an experiment to the one existing database of drugs
     :file: ../../figures/comparison_input.html
 
 
-
-
 Save the plot in a desired format
 ---------------------------------
 

diff --git a/docs/chapters/features/enrichment.rst b/docs/chapters/features/enrichment.rst
@@ -1,7 +1,11 @@
-Kinases inference
-=================
+Kinases inference analysis
+==========================
 
-1. Read your input sequences file. Make sure to have on first column the sequences and on second column the log2 transformed Fold Change.
+1. Read your input file
+
+.. note:: 
+
+    Make sure to have the phospho-sequences on the first column and the log2 transformed Fold Change on the second column.
 
 .. code:: python
 
@@ -17,7 +21,16 @@ Kinases inference
     [464 rows x 2 columns]
     pandas.DataFrame
 
-2. Run enrichment analysis with your input phospho-sequences.
+.. note::
+
+    Data: CK2 catalytic sub-units knockdown
+
+
+2. Run enrichment analysis with your input phospho-sequences
+
+.. note:: 
+
+    Supported methods are ``min``, ``max``, ``avg``, ``all``
 
 .. code:: python
 
@@ -28,7 +41,7 @@ Kinases inference
     Total number of unregulated phospho-sequences is: 309
     enrichment.Enrichment
 
-3. Access the total number of upregulated, downregulated and unregulated phospho-sequences. 
+3. Access the total number of up-regulated, down-regulated, and un-regulated phospho-sequences
 
 .. code:: python
 
@@ -42,15 +55,15 @@ Kinases inference
     309
     int
 
-4. Check the sites that were marked as failed. 
+4. Check the sites that were marked as failed
 
 .. code:: python
 
     >>> enrich.failed_sites
     ['EKIGEGTyGVVYKGR', 'KPSIVTKyVESDDEK', 'LGQRIYQyIQSRFYR', 'INPGYDDyADSDEDQ', 'ADNDITPyLVSRFYR', 'RGEPNVSyICSRYYR']
     list
 
-5. Check the regulation of each sequence and top 15 kinases most likely to target each sequence
+5. Check the regulation of each phospho-sequence, and get the top 15 kinases most likely to target each phospho-sequence
 
 .. code:: python
 
@@ -65,7 +78,7 @@ Kinases inference
     [464 rows x 4 columns]
     pandas.DataFrame
 
-6. Show enrichment table.
+6. Show enrichment table
 
 .. code:: python
 
@@ -82,8 +95,12 @@ Kinases inference
     [303 rows x 19 columns]
     pandas.DataFrame
 
-7. Vulcano plot of enrichment vs p-value. Kinases are represented with colours corresponding to their class. 
+7. Vulcano plot of Enrichment Odds Ratio (EOR) and p-value
+
+.. note::
 
+    Kinases are represented with colours corresponding to their class. 
+
 .. code:: python
 
     >>> fig = enrich.plot(use_adjusted_pval=False)
@@ -95,11 +112,14 @@ Kinases inference
 
 .. note::
 
-    Data: CK2 catalytic sub-units knockdown
+    You can update your figure (marker point, axis, legend, etc.) using Plotly’s functions:
+    `https://plotly.com/python/creating-and-updating-figures <https://plotly.com/python/creating-and-updating-figures>`_
+
+
 
 
 
-8. Save the figure in a desired format.
+8. Save the figure in a desired format
 
 
 - ``.html``

diff --git a/docs/chapters/features/scoring.rst b/docs/chapters/features/scoring.rst
@@ -1,7 +1,7 @@
-Get scores for a sequence
-=========================
+Get scores for a phospho-sequence
+=================================
 
-1. Score a given sequence and store the results.
+1. Score a given phospho-sequence and store the results
 
 .. code:: python
 
@@ -11,11 +11,11 @@ Get scores for a sequence
 
 .. note:: 
 
-    The supported format for a sequence\
+    The supported format for a phospho-sequence\
         - ``asterisk``: F_KQKAS*QSPQK
         - ``(ph)``: FKQKAS(ph)QSPQK
 
-2. Rank the kinases, for a given sequence, based on their percentile score.
+2. Rank the kinases for a given phospho-sequence based on their percentile score
 
 .. code:: python
 
@@ -54,15 +54,15 @@ Get scores for a sequence
     MNK2     8.275760   3.048892            97.455
     pandas.DataFrame
 
-4. Get median percentile. 
+4. Get median percentile (median score of kinases for a given phospho-sequence)
 
 .. code:: python
 
     >>> res.median_percentile
     63.493
     numpy.float64
 
-5. Get promiscuity index. By default, the limit is the 90th percentile.
+5. Get promiscuity index (the number of kinases scoring above the ``90th`` percentile)
 
 .. code:: python
 

diff --git a/docs/chapters/installation.rst b/docs/chapters/installation.rst
@@ -23,18 +23,35 @@ Requirements
 
 .. 	pip install kinex
 
+Installation from Conda
+------------------------
+
+1. Create and activate your conda environment
+
+.. code:: bash
+
+	conda create --name kinex
+	conda activate kinex
+
+2. Install kinex package
+
+.. code:: bash
+
+	conda install -c bioconda kinex
+
+
 Installation from Source
 ------------------------
 
-1. Create and activate a python 3.11 conda venv:
+1. Create and activate a python 3.11 conda environment
 
 .. code:: bash
 
 	conda create --name kinex
 	conda activate kinex
 	conda install python=3.11
 
-2. Download the package:
+2. Download the package
 
 .. code:: bash
 

diff --git a/docs/chapters/usage.rst b/docs/chapters/usage.rst
@@ -30,22 +30,13 @@ Import package and initialise data object
 
     You can optionally save the scoring matrix locally for future uses.
 
-    .. code:: bash
-
-        >>> ### Download scoring matrix of 82k pre-scored sites
-        >>> !mkdir scoring_matrix
-        >>> !wget https://zenodo.org/records/10201142/files/kinex_scoring_matrix_82k_sorted.csv.gzip?download=1 -O scoring_matrix/kinex_scoring_matrix_82k_sorted.csv.gzip
-        >>> !mv scoring_matrix/kinex_scoring_matrix_82k_sorted.csv.gzip scoring_matrix/kinex_scoring_matrix_82k_sorted.csv.gz
-        >>> !gunzip scoring_matrix/kinex_scoring_matrix_82k_sorted.csv.gz
-
     .. code:: python
 
-        >>> ### Read the scoring matrix from file
-        >>> scoring_matrix = pd.read_csv("scoring_matrix/scoring_matrix_82k_sorted.csv")
+        >>> scoring_matrix.to_csv("path/to/scoring_matrix.csv")
 
-    Or just download using the `link <https://zenodo.org/records/10201142/files/kinex_scoring_matrix_82k_sorted.csv.gzip?download=1>`_
+    Or just download using the link: `https://zenodo.org/records/10201142/files/kinex_scoring_matrix_82k_sorted.csv.gzip?download=1 <https://zenodo.org/records/10201142/files/kinex_scoring_matrix_82k_sorted.csv.gzip?download=1>`_
 
-3.  Create a kinex object.
+3.  Create a kinex object
 
 .. code:: python
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -9,7 +9,7 @@
 project = 'Kinex'
 copyright = '2023, Alexandra Valeanu and Jitao David Zhang'
 author = 'Alexandra Valeanu and Jitao David Zhang'
-release = '1.0.1'
+release = '1.0.2'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

diff --git a/docs/index.rst b/docs/index.rst
@@ -6,7 +6,12 @@
 Welcome to Kinex's documentation!
 =================================
 
-This documentation includes the information about installation and usage of the package
+Kinex is a workflow implemented in a Python package with the same name. Kinex infers causal kinases from phosphoproteomics data. 
+
+If you use Kinex, please cite Valeanu et. al, 2023, bioRxiv, doi: `https://doi.org/10.1101/2023.11.23.568445 <https://doi.org/10.1101/2023.11.23.568445>`_.
+
+This documentation includes the information about installation and usage of the package.
+
 
 .. toctree::
    :maxdepth: 3

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name="kinex",
-    version="1.0.1",
+    version="1.0.2",
     description="A python package to compute kinase scoring and enrichment",
     packages=["kinex", "kinex.data", "kinex.tests", "kinex.tests.data"],
     package_dir={"kinex": "src",

diff --git a/src/__init__.py b/src/__init__.py
@@ -1 +1,2 @@
-from kinex.kinex import Kinex
+from kinex.kinex import Kinex
+from kinex.comparison import Comparison