added README and refined docs

RAPDOR/datastructures.py

@@ -438,7 +438,7 @@ def calc_mean_distance(self):
         jsd = self._calc_distance_via(self.state.distance_method, rnase_true, rnase_false, axis=-1)
         self.df["Mean Distance"] = jsd
 
-    def determine_peaks(self, beta: float = 100):
+    def determine_peaks(self, beta: float = 1000):
         """Determines the Mean Distance, Peak Positions and shift direction.
 
         The Peaks are determined the following way:

RAPDOR/plots.py

@@ -948,7 +948,9 @@ def _update_distribution_layout(fig, names, x, offset, yname):
             font=dict(family='SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace', size=16)
 
         )
-
+    )
+    fig.update_layout(
+        showlegend=True
     )
     return fig
 

README.md

@@ -0,0 +1,11 @@
+# RAPDOR
+
+**R**apid **A**NOSIM using **P**robability **D**istance for estimati**O**n of **R**edistribution (RAPDOR) is a 
+package to identify changes in distribution profiles originating from two different conditions. 
+
+## [Getting Started](https://domonik.github.io/RAPDOR/)
+
+For installation details, documentation and various tutorials please have a look at our documentation page here:
+
+https://domonik.github.io/RAPDOR/
+

docs/source/running_dash.rst

@@ -51,16 +51,4 @@ You can upload your design and intensities files that you prepared earlier
 (see :ref:`Data Prepatation<data-prep-tutorial>`) via the upload page.
 
 
-DISPLAY mode
-------------
-
-You can run the app in display mode. This will disable most of the buttons and is ment for displaying pre-analyzed data.
-To achieve this you need to set the environment variable :code:`RAPDOR_DISPLAY_MODE=True`.
-
-.. note::
-
-    You need to add the pre-analyzed data when you run the dash app e.g. via the :code:`--input` flag.
-    Otherwise you can setup your own server (see :ref:`Server Setup<server-setup>`)
-
-