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A pure python code to draw gene diagrams with introns and exons and draw markers ('lollipops') at random positions on the gene
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| 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__ = "parashar.dhapola@gmail.com" | |
| 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() |
FYI - this figure generator plays nicely with mpld3 to generate embeddable d3-based diagrams.
in order to get rid of the TypeError: 'float' object cannot be interpreted as an integer you have to change line 124 to:
minortick_pos = [x for x in range(min_pos, max_pos, int((max_pos-min_pos)/20))][1:]
or use the // (floor division) operator
This is very cool! @parashardhapola I am looking for something like but want it interactive to add my genome wide Bokeh plot. Please let me know if you know of any package or other ideas. Thanks.
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A sample Image generated using this code