Merge pull request #49 from kirichoi/develop

Pull to HEAD

README.md

@@ -4,13 +4,13 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![PyPI version](https://badge.fury.io/py/netplotlib.svg)](https://badge.fury.io/py/netplotlib)
 
-A simple package for visualizing and analyzing reaction network models
+A package for visual analysis of biochemical reaction network models
 
-Copyright 2018-2020 Kiri Choi
+Copyright 2018-2021 Kiri Choi
 
 ## Introduction
 
-Netplotlib is an extension to [NetworkX](https://networkx.github.io/) and [matplotlib](https://matplotlib.org/) to draw and analyze reaction network diagrams in SBML or Antimony strings with ease. Netplotlib supports visualization of quantities such as flux and species rate of change. Netplotlib provides functions to visualize network model ensemble.
+Netplotlib is an extension to [NetworkX](https://networkx.github.io/) and [matplotlib](https://matplotlib.org/) for visual analysis of biochemical reaction network diagrams written in SBML or Antimony strings. Netplotlib supports visualization of quantities such as flux and species rate of change. Netplotlib provides functions to visualize an ensemble of biochemical reaction networks.
 
 ```{python}
 import netplotlib as npl

netplotlib/VERSION.txt

@@ -1 +1 @@
-1.1.0
+1.2.0

netplotlib/layout.py

@@ -0,0 +1,268 @@
+# -*- coding: utf-8 -*-
+"""
+Layout extension support for netplorlib library
+
+Kiri Choi (c) 2021 
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.patches import (FancyArrowPatch, FancyBboxPatch, ArrowStyle, 
+                                Arc, RegularPolygon, Rectangle, PathPatch,
+                                Circle)
+from matplotlib import gridspec, cm, colors
+from matplotlib.path import Path
+from matplotlib.transforms import Bbox
+from matplotlib.text import Text
+from matplotlib.patheffects import AbstractPathEffect
+import libsbml
+
+def getPos(layoutPlugin):
+    """
+    Return the layout of the model
+    
+    :param layoutPlugin: SBML layout plugin
+    :returns pos: Dictionary of all nodes and corresponding coordinates
+    """
+
+    pos = dict()
+
+    layout = layoutPlugin.getLayout(0) # TODO: currently support only the first layout
+
+    for i in range(layout.getNumCompartmentGlyphs()):
+        cg = layout.getCompartmentGlyph(i)
+        bbox = cg.getBoundingBox()
+        cgpos = bbox.getPosition()
+        pos[cg.getCompartmentId()] = np.array([cgpos.x_offset, cgpos.y_offset])
+
+    for i in range(layout.getNumSpeciesGlyphs()):
+        sg = layout.getSpeciesGlyph(i)
+        bbox = sg.getBoundingBox()
+        sgpos = bbox.getPosition()
+        pos[sg.getSpeciesId()] = np.array([sgpos.x_offset, sgpos.y_offset])
+
+    return pos
+
+def stretch_font(text, width, height):
+
+    class TextScaler(AbstractPathEffect):
+
+        def __init__(self, text, width, height):
+            self._text = text
+            self._width = width
+            self._height = height
+
+        def draw_path(self, renderer, gc, tpath, affine, rgbFace=None):
+            ax = self._text.axes
+            renderer = ax.get_figure().canvas.get_renderer()
+            bbox = text.get_window_extent(renderer=renderer)
+            bbox = Bbox(ax.transData.inverted().transform(bbox))
+
+            scale_x = self._width/bbox.width
+            scale_y = self._height/bbox.height
+
+            affine = affine.identity().scale(scale_x, scale_y) + affine
+            renderer.draw_path(gc, tpath, affine, rgbFace)
+
+    text.set_path_effects([TextScaler(text, width, height)])
+
+def draw(NetworkClass, show=True, savePath=None, dpi=150):
+    """
+    Draw network diagram using SBML Layout package
+    
+    :param show: flag to show the diagram
+    :param savePath: path to save the diagram
+    :param dpi: dpi settings for the diagram
+    """
+
+    size = dict()
+
+    fig = plt.figure()
+
+    if NetworkClass.customAxis != None:
+        ax = NetworkClass.customAxis
+    else:
+        ax = plt.gca()
+
+    layout = NetworkClass._Var.layoutPlugin.getLayout(0) # TODO: currently support only the first layout
+
+    layoutCompartmentGlyphIds = []
+    layoutSpeciesGlyphIds = []
+    layoutReactionGlyphIds = []
+    layoutTextGlyphIds = []
+
+    for n in range(layout.getNumCompartmentGlyphs()):
+        cg = layout.getCompartmentGlyph(n)
+        bbox = cg.getBoundingBox()
+        cgpos = bbox.getPosition()
+        layoutCompartmentGlyphIds.append(cg.getCompartmentId())
+
+        dim = bbox.getDimensions()
+        size[cg.getCompartmentId()] = np.array([dim.getWidth(), dim.getHeight()])
+
+        node_color = NetworkClass.compartmentColor
+
+        c = FancyBboxPatch((cgpos.x_offset,
+                            cgpos.y_offset),
+                            dim.getWidth(), 
+                            dim.getHeight(),
+                            boxstyle="round,pad=0.01, rounding_size=0.02",
+                            linewidth=NetworkClass.compartmentEdgelw, 
+                            edgecolor=NetworkClass.compartmentEdgeColor, 
+                            facecolor=node_color,
+                            alpha=0.5)
+
+        ax.add_patch(c)
+
+    for n in range(layout.getNumSpeciesGlyphs()):
+        sg = layout.getSpeciesGlyph(n)
+        bbox = sg.getBoundingBox()
+        sgpos = bbox.getPosition()
+        layoutSpeciesGlyphIds.append(sg.getSpeciesId())
+
+        dim = bbox.getDimensions()
+        size[sg.getSpeciesId()] = np.array([dim.getWidth(), dim.getHeight()])
+
+        if (sg.getSpeciesId() in NetworkClass._Var.boundaryId):
+            node_color = NetworkClass.boundaryColor
+        else:
+            node_color = NetworkClass.nodeColor
+
+        c = FancyBboxPatch((sgpos.x_offset,
+                            sgpos.y_offset),
+                            dim.getWidth(), 
+                            dim.getHeight(),
+                            boxstyle="round,pad=0.01, rounding_size=0.02",
+                            linewidth=NetworkClass.nodeEdgelw, 
+                            edgecolor=NetworkClass.nodeEdgeColor, 
+                            facecolor=node_color)
+
+        NetworkClass._Var.G.nodes[sg.getSpeciesId()]['patch'] = c
+
+        ax.add_patch(c)
+
+    for n in range(layout.getNumReactionGlyphs()):
+        rg = layout.getReactionGlyph(n)
+
+        cg = rg.getCurve()
+
+        for c in range(cg.getNumCurveSegments()):
+            csg = cg.getCurveSegment(c)
+            if type(csg) == libsbml.LineSegment:
+                csgs = csg.getStart()
+                csge = csg.getEnd()
+
+                e = PathPatch(Path([(csgs.getXOffset(), csgs.getYOffset()), 
+                                    (csge.getXOffset(), csge.getYOffset())], 
+                                   [Path.MOVETO, Path.LINETO]), 
+                              color=NetworkClass.reactionColor,
+                              lw=(1+NetworkClass.edgelw))
+            else:
+                csgs = csg.getStart()
+                csge = csg.getEnd()
+                csgcp1 = csg.getBasePoint1()
+                csgcp2 = csg.getBasePoint2()
+
+                e = FancyArrowPatch(path=Path([(csgs.getXOffset(), csgs.getYOffset()),
+                                        (csgcp1.getXOffset(), csgcp1.getYOffset()),
+                                        (csgcp2.getXOffset(), csgcp2.getYOffset()),
+                                        (csge.getXOffset(), csge.getYOffset())], 
+                                       [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]), 
+                                  color=NetworkClass.reactionColor,
+                                  lw=(1+NetworkClass.edgelw))
+            ax.add_patch(e)
+
+        for b in range(rg.getNumSpeciesReferenceGlyphs()):
+            srg = rg.getSpeciesReferenceGlyph(b)
+            srgc = srg.getCurve()
+
+            if srg.getRoleString() == 'substrate':
+                arrowstyle = ArrowStyle.Curve()
+            elif srg.getRoleString() == 'sidesubstrate':
+                arrowstyle = ArrowStyle.Curve()
+            elif srg.getRoleString() == 'product':
+                arrowstyle = ArrowStyle.CurveFilledB(head_length=2.5*NetworkClass.edgelw, head_width=2*NetworkClass.edgelw)
+            elif srg.getRoleString() == 'sideproduct':
+                arrowstyle = ArrowStyle.CurveFilledB(head_length=2.5*NetworkClass.edgelw, head_width=2*NetworkClass.edgelw)
+            elif srg.getRoleString() == 'activator':
+                arrowstyle = ArrowStyle.Curve()
+            elif srg.getRoleString() == 'inhibitor':
+                arrowstyle = ArrowStyle.BarAB(widthA=0.0, angleA=None, widthB=3*NetworkClass.edgelw, angleB=None)
+            else:
+                arrowstyle = ArrowStyle.Curve()
+
+            for bc in range(srgc.getNumCurveSegments()):
+                srgcs = srgc.getCurveSegment(bc)
+                if type(srgcs) == libsbml.LineSegment:
+                    srgcss = srgcs.getStart()
+                    srgcse = srgcs.getEnd()
+
+                    e = FancyArrowPatch(path=Path([(srgcss.getXOffset(), srgcss.getYOffset()), 
+                                        (srgcse.getXOffset(), srgcse.getYOffset())], 
+                                       [Path.MOVETO, Path.LINETO]),
+                                  arrowstyle=arrowstyle,
+                                  color=NetworkClass.reactionColor,
+                                  lw=(1+NetworkClass.edgelw))
+
+                else:
+                    srgcss = srgcs.getStart()
+                    srgcse = srgcs.getEnd()
+                    srgcscp1 = srgcs.getBasePoint1()
+                    srgcscp2 = srgcs.getBasePoint2()
+
+                    e = FancyArrowPatch(path=Path([(srgcss.getXOffset(), srgcss.getYOffset()),
+                                            (srgcscp1.getXOffset(), srgcscp1.getYOffset()),
+                                            (srgcscp2.getXOffset(), srgcscp2.getYOffset()),
+                                            (srgcse.getXOffset(), srgcse.getYOffset())], 
+                                           [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]), 
+                                        arrowstyle=arrowstyle,
+                                        color=NetworkClass.reactionColor,
+                                        lw=(1+NetworkClass.edgelw))
+
+                ax.add_patch(e)
+
+            if srg.getRoleString() == 'activator':
+                e = Circle((srgcse.getXOffset(), srgcse.getYOffset()),
+                           radius=3*NetworkClass.edgelw,
+                           color=NetworkClass.reactionColor,
+                           lw=(1+NetworkClass.edgelw))
+                ax.add_patch(e)
+
+    for n in range(layout.getNumTextGlyphs()):
+        tg = layout.getTextGlyph(n)
+        bbox = tg.getBoundingBox()
+        tgpos = bbox.getPosition()
+        speciesName = NetworkClass._Var.sbmlmodel.getSpecies(tg.getOriginOfTextId())
+        if speciesName != None:
+            if speciesName.getName() != '':
+                speciesName = speciesName.getName()
+            else:
+                speciesName = speciesName.getId()
+        else:
+            sg = layout.getSpeciesGlyph(tg.getOriginOfTextId())
+            speciesName = sg.getSpeciesId()
+        layoutTextGlyphIds.append(speciesName)
+
+        dim = bbox.getDimensions()
+
+        mattext = ax.text(tgpos.x_offset, tgpos.y_offset, speciesName,
+                          horizontalalignment='left', verticalalignment='bottom',
+                          color=NetworkClass.labelColor)
+
+        stretch_font(mattext, dim.getWidth(), dim.getHeight())
+
+    layoutDim = layout.getDimensions()
+    plt.xlim(0, layoutDim.getWidth())
+    plt.ylim(0, layoutDim.getHeight())
+    plt.axis('off')
+    plt.show()
+
+    if savePath != None:
+        try:
+            fig.savefig(savePath, bbox_inches='tight', dpi=dpi)
+        except IOError as e:
+            raise Exception("Error saving diagram: " + str(e))
+
+    if show and NetworkClass.customAxis == None:
+        plt.show()
+    plt.close()