icedevil2001 · August 17, 2017 13:41 · Aug 5, 2016 · Aug 5, 2016
diff --git a/GeneImage.py b/GeneImage.py
@@ -1,5 +1,29 @@
 import matplotlib.pyplot as plt
 
+"""
+MIT License
+Copyright (c) [2016] [Parashar Dhapola]
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+
+__author__ = "Parashar Dhapola"
+__email__ = "[email protected]"
+
+
 class GeneImage(object):
     def __init__(self, exon_intervals, marker_pos=[], marker_heights=[], marker_colors=[],
                  marker_size=100, marker_weight=1.5, exon_color="black", intron_color="grey",

diff --git a/GeneImage.py b/GeneImage.py
@@ -0,0 +1,132 @@
+import matplotlib.pyplot as plt
+
+class GeneImage(object):
+    def __init__(self, exon_intervals, marker_pos=[], marker_heights=[], marker_colors=[],
+                 marker_size=100, marker_weight=1.5, exon_color="black", intron_color="grey",
+                 intron_weight=2, intron_style='-', bar_color='cornflowerblue', bg_color="white"):
+        self.exonIntervals = exon_intervals
+        self.markerPositions = marker_pos
+        self.markerHeights = marker_heights
+        self.markerColors = marker_colors
+        self.markerSize = marker_size
+        self.MarkerWeight = marker_weight
+        self.exonColor = exon_color
+        self.intronColor = intron_color
+        self.intronWeight = intron_weight
+        self.intronStyle = intron_style
+        self.barColor= bar_color
+        self.bgColor = bg_color
+        self.markerDefaultColor = 'grey'
+        self.numExons = len(self.exonIntervals)
+        self.totalSpan = self.exonIntervals[-1][1] - self.exonIntervals[0][0]
+        self.minExonLen = self.totalSpan*0.005
+        self.ylims = {'exon_max': 2, 'exon_min':1}
+        self.figure, self.canvas = plt.subplots(figsize=(15,1.5))
+        self.canvas.set_axis_bgcolor(self.bgColor)
+        self._draw()
+
+    def _set_limits(self):
+        self.ylims['intron_max'] = self.ylims['exon_max']*0.9
+        self.ylims['intron_min'] = (self.ylims['exon_max'] + self.ylims['exon_min'])/2.0
+        self.ylims['bar_min'] = self.ylims['exon_max']+0.2
+        self.ylims['bar_max'] = self.ylims['bar_min']+(self.ylims['exon_max']-self.ylims['exon_min'])/5.0
+
+
+    def _transform_spans(self):
+        span_lens = [x[1]-x[0] for x in self.exonIntervals]
+        max_len = float(max(span_lens))
+        transformed_intervals = []
+        if max_len < self.minExonLen:
+            span_ratios = [x/max_len for x in span_lens]
+            expansion_factor = self.totalSpan*1e-11
+            for i in range(1,10):
+                ef = (2**i)*expansion_factor
+                if max_len+ef > self.minExonLen:
+                    expansion_factor = ef
+                    break
+            for i,j in zip(self.exonIntervals, span_ratios):
+                mid = (i[0] + i[1])/2
+                f = (expansion_factor*j)/2
+                if mid+f - mid-f > self.minExonLen:
+                    transformed_intervals.append([mid-f, mid+f])
+                else:
+                    transformed_intervals.append([mid-(self.minExonLen/2), mid+(self.minExonLen/2)])
+        else:
+            for i in range(self.numExons):
+                if span_lens[i] < self.minExonLen:
+                    mid = (self.exonIntervals[i][0] + self.exonIntervals[i][0])/2 
+                    transformed_intervals.append([mid-(self.minExonLen/2), mid+(self.minExonLen/2)])
+                else:
+                    transformed_intervals.append(self.exonIntervals[i])
+        self.exonIntervals = transformed_intervals[:]
+
+    def _draw_exon(self, span):
+        self.canvas.fill_between(span, self.ylims['exon_min'], self.ylims['exon_max'],
+                                 edgecolor=self.bgColor, facecolor=self.exonColor)
+        return True
+
+    def _draw_intron(self, span):
+        mid = (span[0]+span[1])/2.0
+        self.canvas.plot([span[0], mid], [self.ylims['intron_min'], self.ylims['intron_max']],
+                         c=self.intronColor, lw=self.intronWeight, ls=self.intronStyle)
+        self.canvas.plot([mid, span[1]], [self.ylims['intron_max'], self.ylims['intron_min']],
+                         c=self.intronColor, lw=self.intronWeight, ls=self.intronStyle)
+        return True
+
+    def _draw_markers(self):
+        if self.markerHeights == []:
+            self.markerHeights = [self.ylims['exon_max']-self.ylims['exon_min'] for x in self.markerPositions]
+        if self.markerColors == []:
+            self.markerColors = [self.markerDefaultColor for x in self.markerPositions]           
+        for p,h,c in zip(self.markerPositions, self.markerHeights, self.markerColors):
+            self.canvas.plot((p, p), (self.ylims['bar_max'], self.ylims['bar_max']+h),
+                             linestyle='-', color='black', linewidth=self.MarkerWeight, alpha=0.7)
+            self.canvas.scatter(p, self.ylims['bar_max']+h+0.25, s=self.markerSize, marker='o', c=c,
+                                edgecolor=c, alpha=1)
+
+
+    def _clean_axes(self):
+        #self.canvas.set_ylim((self.ylims['exon_min'], self.ylims['bar_max']))
+        self.canvas.set_yticks([], [])
+        self.canvas.get_xaxis().tick_top()
+        self.canvas.tick_params(axis='x', direction='out')
+        self.canvas.set_xticks([])
+        for o in ["top", "bottom", "left", "right"]:
+            self.canvas.spines[o].set_visible(False)
+        min_pos = int(self.exonIntervals[0][0] - self.totalSpan * 0.1)
+        if min_pos < 0:
+            min_pos = 0
+        max_pos = int(self.exonIntervals[-1][1] + self.totalSpan * 0.1)
+        minortick_pos = [x for x in range(min_pos, max_pos, (max_pos-min_pos)/20)][1:]
+        for i in minortick_pos:
+            self.canvas.axvline(i, alpha=0.2, c='black', ls='--')
+        self.canvas.text(minortick_pos[0], self.ylims['exon_min']-0.5,
+                         minortick_pos[0], fontsize=8, ha='center')
+        self.canvas.text(minortick_pos[-1], self.ylims['exon_min']-0.5,
+                         minortick_pos[-1], fontsize=8, ha='center')
+        self.canvas.set_xlim(minortick_pos[0]-(minortick_pos[1]-minortick_pos[0]),
+                             minortick_pos[-1]+(minortick_pos[-1]-minortick_pos[-2]))
+
+    def _draw(self):
+        self._set_limits()
+        self._transform_spans()
+        for i in range(self.numExons):
+            if i > 0:
+                self._draw_intron([self.exonIntervals[i-1][1], self.exonIntervals[i][0]])
+            self._draw_exon(self.exonIntervals[i])
+        self.canvas.fill_between([self.exonIntervals[0][0], self.exonIntervals[-1][1]],
+                                  self.ylims['bar_min'], self.ylims['bar_max'],
+                                  edgecolor=self.bgColor, facecolor=self.barColor)
+        self._draw_markers()
+        self._clean_axes()
+
+    def show(self):
+        plt.show()
+
+if  __name__ == "__main__":
+    #exons positions
+    exon_pos = [97543299,97544702], [97547885,97548026], [97564044,97564188], [97658624,97658804], [97700407,97700550], [97770814,97770934], [97771732,97771853], [97839116,97839200], [97847948,97848017], [97915614,97915779], [97981281,97981497], [98015115,98015300], [98039315,98039526], [98058773,98058943], [98060614,98060722], [98144650,98144738], [98157272,98157354], [98164906,98165103], [98187065,98187227], [98205947,98206035], [98293669,98293752], [98348819,98348930], [98386439,98386615]
+    #marker positions
+    marker_pos = [97947885, 98247485]
+    gene = GeneImage(exon_pos, marker_pos)
+    gene.show()