Merge pull request #8 from domonik/dev

Dev

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Dominik Rabsch
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

RAPDOR/visualize/callbacks/mainCallbacks.py

@@ -275,8 +275,9 @@ def display_mode_alert(uid, display_mode):
             [
                 html.H3("Display mode", style={"color": "white"}),
                 html.Div([
-                    "This is ment to inspect pre-analyzed data. The tool for data analysis can be downloaded here: ",
-                    html.A("https://github.com/domonik/RAPDOR/releases", target="_blank", href="https://github.com/domonik/RAPDOR/releases", id="displayModeLink")
+                    "This is ment to inspect pre-analyzed data. You can download the tool for data analysis here: ",
+                    html.Br(),
+                    html.A("https://github.com/domonik/RAPDOR/releases", target="_blank", href="https://github.com/domonik/RAPDOR/releases", id="displayModeLink", style={"line-break": "anywhere"})
                 ])
             ]
         )
@@ -287,7 +288,7 @@ def display_mode_alert(uid, display_mode):
                 color="var(--primary-color)",
                 dismissable=True,
             ),
-            className="p-2 align-items-center, alert-msg",
+            className="p-2 align-items-center, alert-msg col-md-5 col-12",
 
         )
         return False, alert_msg

README.md

@@ -5,7 +5,88 @@ package to identify changes in distribution profiles originating from two differ
 
 ## [Getting Started](https://domonik.github.io/RAPDOR/)
 
-For installation details, documentation and various tutorials please have a look at our documentation page here:
+For latest installation details, documentation and various tutorials please have a look at our documentation page here:
 
 https://domonik.github.io/RAPDOR/
 
+# Minimal documentation
+## System requirements
+
+### Hardware requirements
+
+`RAPDOR` only requires a standard computer with sufficient RAM depending on the analyzed dataset. 
+
+### Software requirements
+
+#### OS
+
+`RAPDOR` is supported for *Windows*, *macOS* and *Linux* and is constantly tested via  GitHub actions for the following
+systems:
+
+- Linux: Ubuntu 22.04
+
+####  Dependencies
+
+`RAPDOR` requires `Python 3` and `pip` to be installed. It is tested for Python versions `3.10` to `3.12`.
+
+Note that there is an issue with a dependency that disallows the use of Python `3.13` at the current state
+
+
+```text
+statsmodels,
+numpy
+scipy
+plotly>=5.16
+pandas
+dash>=2.5
+dash_bootstrap_components
+scikit-learn
+dash_loading_spinners
+kaleido
+dash_daq
+dash_extensions
+pyYAML
+dash[diskcache]
+```
+
+## Installation
+
+## Install from PyPi
+
+We highly reccomend to install RAPDOR into a fresh setup conda environment that only contains a supported Python 
+version. This usually avoids dependency conflicts.
+
+
+```shell
+conda create -n rapdor_env
+conda activate rapdor_env
+conda install python==3.12
+```
+
+```shell
+pip3 install RAPDOR
+```
+
+Installing RAPDOR usually takes less than a minute.
+
+## Demo
+
+### GUI
+
+The following tutorial shows how to run the graphical user interface:
+
+https://domonik.github.io/RAPDOR/v0.1.5/running_dash.html
+
+The graphical user interface itself has in inbuilt demo that can be accessed via clicking the Tutorial button in the
+upper right corner. 
+
+### Python
+
+If you want to learn how to analyze data using the Python API itself please follow:
+
+https://domonik.github.io/RAPDOR/v0.1.5/python_analysis.html
+
+
+
+
+

docs/source/installation.rst

@@ -7,24 +7,6 @@ Linux or Windows
 ****************
 
 
-Executable
-----------
-
-.. warning::
-    Executables are highly experimental. Depending on your OS and installed libraries they might not work.
-    We can not guarantee that they work for your computer setup. Thus, we recommend installing the pip package instead.
-
-We provide executable versions of the tool for some operating systems (OS).
-If you are not familiar with virtual environments and the command line you can use the RAPDOR them.
-Those are provided via github. You can get the latest versions for your OS via the assets dropdown here:
-
-`https://github.com/domonik/RAPDOR/releases <https://github.com/domonik/RAPDOR/releases>`_
-
-Please read the instructions in the following tutorial in order to run the tool:
-
-:ref:`Using Executables<executable-tutorial>`
-
-
 
 Pip
 ---
@@ -45,14 +27,29 @@ You can install RAPDOR via:
 
     pip install RAPDOR
 
-Conda
------
 
-Building a conda package is in planning but not done yet
+
+Executable
+----------
+
+.. warning::
+    Executables are highly experimental. Depending on your OS and installed libraries they might not work.
+    We can not guarantee that they work for your computer setup. Thus, we recommend installing the pip package instead.
+
+We provide executable versions of the tool for some operating systems (OS).
+If you are not familiar with virtual environments and the command line you can use RAPDOR via them.
+Those are provided via github. You can get the latest versions for your OS via the assets dropdown here:
+
+`https://github.com/domonik/RAPDOR/releases <https://github.com/domonik/RAPDOR/releases>`_
+
+Please read the instructions in the following tutorial in order to run the tool:
+
+:ref:`Using Executables<executable-tutorial>`
+
 
 
 macOS
 *****
 
-You can install it just like in linux. However, there are no executables for macOS available. Consequently, you need to
+You can install it just like in linux via pip. However, there are no executables for macOS available. Consequently, you need to
 use the command line.

docs/source/python_analysis.rst

@@ -36,14 +36,33 @@ of size 3.
 
 Since we only have 3 replicates per condition for this dataset, it is not reasonable to calculate a p-value. Instead we
 will calculate stats like the Jensen-Shannon-Distance of the means and the ANOSIM R value. We will then rank the table
-based on the R value and the mean distance. This is done via:
+based on the R value and the mean distance, which only takes a second for the test data. This is done via:
 
 .. code-block:: python
 
     rapdordata.calc_all_scores()
     rapdordata.rank_table(["ANOSIM R", "Mean Distance"], ascending=[False, False])
 
+You can always check your calculated parameters via accessing the `rapdordata.extra_df` or the `rapdordata.df` fields.
+The df contains also the data columns and might be messy. For the test data you can print the head of the table:
 
+.. code-block:: python
+
+    print(rapdordata.extra_df.head())
+
+The output should look as follows:
+
+.. code-block::
+
+       id  RAPDORid  ...  position strongest shift  Rank
+    0   0      1118  ...                      10.0    12
+    1   1      1115  ...                       4.0     7
+    2   2      1114  ...                       2.0     1
+    3   3      1721  ...                       7.0     2
+    4   4      1103  ...                       6.0     8
+    [5 rows x 12 columns]
+
+You can see that the protein with the RAPDORid 1114 is ranked on place 1.
 
 Finally we want to export the file as a csv table and as a JSON file. The JSON is further needed to display your data in
 a Dash webserver interface. You can learn more about it in the :ref:`server setup section<server-setup>`.