Added symbols

.gitignore

@@ -58,3 +58,4 @@ docs/_build/
 
 # PyBuilder
 target/
+.vscode/settings.json

README.md

@@ -1,3 +1,5 @@
+pip install --upgrade --no-deps git+git://github.com/dr3y/dnaplotlib.git@master
+
 # 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.
@@ -12,8 +14,10 @@ The DNAplotlib library is contained within the `dnaplotlib.py` file in the `lib`
 ## 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:
 
+### Gallery of all part glyphs
+<a href="gallery/all_parts"><img src="gallery/all_parts/actually_all_parts.png" height="700px"/></a>
+
 ### 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>

gallery/all_parts/README.md

@@ -1,6 +1,6 @@
 # SBOL Visual Parts & Customization
 
-<img src="all_parts.png" width="600px"/>
+<img src="actually_all_parts.png" width="600px"/>
 
-Illustration of all SBOL Visual parts in forward and reverse direction. Each part can have its apperance customised to convay further information.
+Illustration of all SBOL Visual parts in forward and reverse direction. Each part can have its apperance customised to convey further information.
 

gallery/all_parts/actually_all_parts.py

@@ -0,0 +1,39 @@
+#import sys
+import dnaplotlib as dpl
+import matplotlib.pyplot as plt
+#import matplotlib.transforms as mtransforms
+#import matplotlib.patches as mpatch
+#from matplotlib.patches import FancyBboxPatch
+import numpy as np
+
+dnaline = 3
+dr = dpl.DNARenderer(scale = 5,linewidth=dnaline)
+part_renderers = dr.SBOL_part_renderers()
+parts = part_renderers.keys()
+dontrender = ['StemTop']
+fig1 = plt.figure(figsize=(14,14))
+faxes = fig1.subplots(ncols=6,nrows=6)
+raxes = np.ravel(faxes)
+#print(raxes)
+raxind = 0
+for part in parts:
+    if(part in dontrender):
+        continue
+    ax = raxes[raxind]
+    raxind+=1
+    #plt.Figure(figsize=(.1,.1))
+    #ax = plt.gca()
+    design = [{'type':part, 'name':'test', 'fwd':True,\
+               'opts':{'label':part,'label_size':13,'label_y_offset':-8,'color':(.5,.5,.2)}},
+             {'type':part, 'name':'testr', 'fwd':False,'opts':{'color':(.2,.5,.5)}}]
+    start,end = dr.renderDNA(ax,design,part_renderers)
+    ax.axis('off')
+    xdist = end-start
+    delta = xdist*.2
+    start-=delta
+    end+=delta
+    newxdist = end-start
+    ax.set_xlim([start,end])
+
+    ax.set_ylim([-newxdist/2,newxdist/2])
+plt.savefig("actually_all_parts.png")

requirements.txt

@@ -1,2 +1,3 @@
 matplotlib>=1.5.0
 pysbol2
+numpy