Merge pull request #10 from Zsailer/datamodel

Clean up core logic

README.md

@@ -1,16 +1,18 @@
 
-# Python API for analyzing and manipulating genotype-phenotype maps
-
+# GPMap
 
 [![Join the chat at https://gitter.im/harmslab/gpmap](https://badges.gitter.im/harmslab/gpmap.svg)](https://gitter.im/harmslab/gpmap?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![Documentation Status](https://readthedocs.org/projects/gpmap/badge/?version=latest)](http://gpmap.readthedocs.io/en/latest/?badge=latest)
 
-This package defines a standard data-structure for genotype-phenotype (GP) map data.
-Subset, manipulate, extend, etc. GP maps. Calculate statistics, model evolutionary
-trajectories, predict phenotypes (in combination with the epistasis package). Efficient memory usage,
-using numpy arrays to store in memory.
+*A Python API for managing genotype-phenotype map data*
+
+GPMap defines a flexible object for managing genotype-phenotype (GP) map data. At it's core,
+it stores all data in Pandas DataFrames and thus, interacts seamlessly with the
+PyData egosystem.
+
+To visualize genotype-phenotype objects created by GPMap, checkout [GPGraph](https://github.com/Zsailer/gpgraph).
 
-<img src="docs/_img/gpm.png" align="middle">
+<img src="docs/_img/gpm.png"> <img src="docs/_img/dataframe.png" width="400">
 
 ## Basic example
 
@@ -19,7 +21,28 @@ Import the package's base object.
 from gpmap import GenotypePhenotypeMap
 ```
 
-Load a dataset from disk.
+Pass your data to the object.
+```python
+
+# Data
+wildtype = "AAA"
+genotypes = ["AAA", "AAT", "ATA", "TAA", "ATT", "TAT", "TTA", "TTT"]
+phenotypes = [0.1, 0.2, 0.2, 0.6, 0.4, 0.6, 1.0, 1.1]
+stdeviations = [0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05]
+
+# Initialize the object
+gpm = GenotypePhenotypeMap(wildtype,
+                           genotypes,
+                           phenotypes,
+                           stdeviations=stdeviations)
+
+# Check out the data.
+gpm.data
+```
+<img src="docs/_img/dataframe.png" width="350">
+
+
+Or load a dataset from disk.
 ```python
 gpm = GenotypePhenotypeMap.read_json("data.json")
 ```
@@ -38,3 +61,4 @@ pip install -e .
 The following modules are required. Also, the examples/tutorials are written in Jupyter notebooks and require IPython to be install.
 
 * [Numpy](http://www.numpy.org/)
+* [Pandas](https://pandas.pydata.org/)