Permalink
Browse files

Updating READMEs

  • Loading branch information...
chofski committed Apr 12, 2017
1 parent a53e3d6 commit 908263dcebcdf865c1449c751a65724c166a5601
@@ -1,6 +1,6 @@
#DNAplotlib
# DNAplotlib

DNAplotlib is a library that enables highly customizable visualization of individual genetic constructs and libraries of design variants. It can be thought of in many ways as matplotlib for genetic diagrams. Publication quality vector-based output is produced and all aspects of the rendering process can be easily customized or replaced by the user. DNAplotlib is capable of SBOL Visual compliant diagrams in addition to a format able to better illustrate the precise location and length of each genetic part. This alternative "traced-based" visualization method enables direct comparison with nucleotide-level information such as RNA-seq read depth or other base resolution measures. While it is envisaged that access will be predominantly via the programming interface, several easy to use text-based input formats can be processed by a command-line scripts to facilitate broader usage. DNAplotlib is cross-platform and open-source software released under the OSI OSL-3.0 license.

#Dependences
## Dependences
NumPy, matplotlib, pySBOL (optional)
@@ -2,32 +2,32 @@

DNAplotlib is a library that enables highly customizable visualization of individual genetic constructs and libraries of design variants. It can be thought of in many ways as matplotlib for genetic diagrams. Publication quality vector-based output is produced and all aspects of the rendering process can be easily customized or replaced by the user. DNAplotlib is capable of SBOL Visual compliant diagrams in addition to a format able to better illustrate the precise location and length of each genetic part. This alternative "traced-based" visualization method enables direct comparison with nucleotide-level information such as RNA-seq read depth or other base resolution measures. While it is envisaged that access will be predominantly via the programming interface, several easy to use text-based input formats can be processed by a command-line scripts to facilitate broader usage. DNAplotlib is cross-platform and open-source software released under the OSI OSL-3.0 license.

##Installation
## Installation
The DNAplotlib library is contained within the `dnaplotlib.py` file in the `lib` directory and requires Python 2.6 and matplotlib 1.2 or newer. To install add the location of this file to your `PYTHONPATH` and you are good to: `import dnaplotlib`

##Getting Started
## Getting Started
We provide an extensive gallery of use cases for DNAplotlib in the `gallery` directory. Click on a thumbnail below to go directly to the example code:

###Genetic Designs and Annotation
### Genetic Designs and Annotation
<a href="gallery/all_parts"><img src="gallery/all_parts/all_parts.png" height="160px"/></a>
<a href="gallery/xnor_truthtable"><img src="gallery/xnor_truthtable/xnor_truthtable.png" height="160px"/></a>
<a href="gallery/scatter_annotate"><img src="gallery/scatter_annotate/scatter_annotate.png" height="160px"/></a>
<a href="gallery/offset_features"><img src="gallery/offset_features/offset_features_y_offset.png" height="80px"/></a>
<a href="gallery/annotate_design"><img src="gallery/annotate_design/annotate_design.png" height="60px"/></a>
<a href="gallery/input_gff"><img src="gallery/input_gff/input_gff.png" height="50px"/></a>

###New Part Types and Regulation
### New Part Types and Regulation
<a href="gallery/recombinase_not_gate"><img src="gallery/recombinase_not_gate/recombinase_not_gate.png" height="160px"/></a>
<a href="gallery/recombinase_array"><img src="gallery/recombinase_array/recombinase_array.png" height="160px"/></a>

###Trace-based Rendering
### Trace-based Rendering
<a href="gallery/multiple_traces"><img src="gallery/multiple_traces/multiple_traces.png" height="200px"/></a>
<a href="gallery/rotated_design"><img src="gallery/rotated_design/rotated_design.png" height="200px"/></a>
<a href="gallery/input_bed"><img src="gallery/input_bed/input_bed.png" height="200px"/></a>

###Dynamics and Evolution
### Dynamics and Evolution
<a href="gallery/repressilator_animate"><img src="gallery/repressilator_animate/repressilator_animate.png" height="380px"/></a>

###Variant Libraries
### Variant Libraries
<a href="gallery/variants_library"><img src="gallery/variants_library/variants_library.png" height="500px"/></a>
<a href="gallery/order_orientation_library"><img src="gallery/order_orientation_library/order_orientation_library.png" height="500px"/></a>
@@ -1,4 +1,4 @@
#SBOL Visual Parts & Customization
# SBOL Visual Parts & Customization

<img src="all_parts.png" width="600px"/>

@@ -1,4 +1,4 @@
#Annotate Design
# Annotate Design

<img src="annotate_design.png" width="400px"/>

@@ -1,4 +1,4 @@
#Input BED
# Input BED

<img src="input_bed.png" width="400px"/>

@@ -1,4 +1,4 @@
#Input GFF
# Input GFF

<img src="input_gff.png" width="400px"/>

@@ -1,4 +1,4 @@
#Multiple Traces
# Multiple Traces

<img src="multiple_traces.png" width="400px"/>

@@ -1,4 +1,4 @@
#Offset multiple features
# Offset multiple features

<img src="offset_features_y_offset.png" width="400px"/>

@@ -1,4 +1,4 @@
#Order and Orientation Library
# Order and Orientation Library

<img src="order_orientation_library.png" width="400px"/>

@@ -1,4 +1,4 @@
#Recombinase Memory Array
# Recombinase Memory Array

<img src="recombinase_array.png" width="400px"/>

@@ -1,4 +1,4 @@
#Recombinase NOT-gate
# Recombinase NOT-gate

<img src="recombinase_not_gate.png" width="400px"/>

@@ -1,4 +1,4 @@
#Repressilator Animation
# Repressilator Animation

<img src="repressilator_animate.png" width="400px"/>

@@ -1,4 +1,4 @@
#Rotated Design
# Rotated Design

<img src="rotated_design.png" width="400px"/>

@@ -1,4 +1,4 @@
#SBOL Visual
# SBOL Visual

<img src="sbol_visual.png" width="400px"/>

@@ -1,4 +1,4 @@
#Annotated Scatter
# Annotated Scatter

<img src="scatter_annotate.png" width="400px"/>

@@ -1,4 +1,4 @@
#Sequence Features
# Sequence Features

<img src="sequence_features.png" width="400px"/>

@@ -1,4 +1,4 @@
#Library of Design Variants
# Library of Design Variants

<img src="variants_library.png" width="400px"/>

@@ -1,4 +1,4 @@
#XNOR Truthtable
# XNOR Truthtable

<img src="xnor_truthtable.png" width="400px"/>

0 comments on commit 908263d

Please sign in to comment.