update readme

README.md

@@ -4,3 +4,36 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://kchu25.github.io/PlotPWM.jl/dev/)
 [![Build Status](https://github.com/kchu25/PlotPWM.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/kchu25/PlotPWM.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/kchu25/PlotPWM.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/kchu25/PlotPWM.jl)
+
+
+# Usage
+
+```
+using PlotPWM
+
+# Given a position frequency matrix (each column sum to 1)
+
+pfm =  [0.01  1.0  0.98  0.0   0.0   0.0   0.98  0.0   0.18  1.0
+        0.98  0.0  0.01  0.19  0.0   0.96  0.01  0.89  0.03  0.0
+        0.0   0.0  0.0   0.77  0.01  0.0   0.0   0.0   0.56  0.0
+        0.0   0.0  0.0   0.05  0.99  0.04  0.01  0.11  0.24  0.0]
+
+logoplot(pfm)
+```
+will give
+
+![pfm](demo/demo.png)
+
+# Note
+
+The information content $IC(\cdot)$ (i.e. the "letter height") of the $i$-th column $c_i$ in a position weight matrix (PWM) is 
+
+$$
+IC(c_i) = \sum_{\alpha}\,f_{\alpha i}\,\log_2 \frac{f_{\alpha i}}{\beta_\alpha}
+$$
+
+where $f_{\alpha i}$ the frequency of nucleotide $\alpha\in\{A,C,G,T\}$ at the $i$-th column of a PWM. The $4$-dimensional vector $\beta$ is the assumed genomic background
+
+By default, the background $\beta$ is assumed to be flat, i.e. $\beta=(0.25, 0.25,0.25,0.25)$.
+
+