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"""Manages GO Term fill colors and bordercolors.""" |
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__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved." |
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__author__ = "DV Klopfenstein" |
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import collections as cx |
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from goatools.gosubdag.utils import get_kwargs |
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class Go2Color(object): |
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"""Manages GO Term fill colors and bordercolors.""" |
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kws_dct = set(['go2color', 'go2bordercolor', 'dflt_bordercolor', 'key2col']) |
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alpha2col = cx.OrderedDict([ |
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# GOEA GO terms that are significant |
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(0.005, 'mistyrose'), |
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(0.010, 'moccasin'), |
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(0.050, 'lemonchiffon1'), |
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# GOEA GO terms that are not significant |
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(1.000, 'grey95'), |
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]) |
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key2col = { |
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'level_01': '#f1fbfd', # Very light blue |
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'go_sources': '#ffffe4', # xkcd off white |
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'go_leafchild': '#eae8e8', # 'Grey palette' http://www.color-hex.com/color-palette/45491 |
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} |
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def __init__(self, gosubdag, objgoea=None, **kws): |
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# kws: go2color go2bordercolor dflt_bordercolor |
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self.kws = get_kwargs(kws, self.kws_dct, None) |
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# Use default key coloring if user does not specify to turn it off (key2col=False) |
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if 'key2col' not in kws or kws['key2col']: |
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self.kws['key2col'] = self.key2col |
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self.gosubdag = gosubdag # GoSubDag |
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self.objgoea = objgoea # GoeaResults |
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self.dflt_bordercolor = kws.get('dflt_bordercolor', 'mediumseagreen') |
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self.go2color = self.init_goid2color() |
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self.go2bordercolor = kws.get('go2bordercolor', {}) |
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self._init_equiv() |
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def get_bordercolor(self, goid): |
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"""Return GO Term border color.""" |
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return self.go2bordercolor.get(goid, self.dflt_bordercolor) |
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def init_goid2color(self): |
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"""Set colors of GO terms.""" |
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goid2color = {} |
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# 1. User-specified colors for each GO term |
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if 'go2color' in self.kws: |
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for goid, color in self.kws['go2color'].items(): |
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goid2color[goid] = color |
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# 2. colors based on p-value override colors based on source GO |
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if self.objgoea is not None: |
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self.objgoea.set_goid2color_pval(goid2color) |
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key2color = self.kws.get('key2col') |
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if key2color is not None: |
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# 3. Default GO source color |
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if 'go_sources' in key2color: |
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color = key2color['go_sources'] |
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go2obj = self.gosubdag.go2obj |
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for goid in self.gosubdag.go_sources: |
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if goid not in goid2color: |
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goobj = go2obj[goid] |
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goid2color[goobj.id] = color |
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goid2color[goid] = color |
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# 4. Level-01 GO color |
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if 'level_01' in key2color: |
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color = key2color['level_01'] |
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for goid, goobj in self.gosubdag.go2obj.items(): |
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if goobj.level == 1: |
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if goid not in goid2color: |
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goid2color[goid] = color |
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return goid2color |
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def _init_equiv(self): |
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"""Add equivalent GO IDs to go2color, if necessary.""" |
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gocolored_all = set(self.go2color) |
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go2obj_usr = self.gosubdag.go2obj |
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go2color_add = {} |
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for gocolored_cur, color in self.go2color.items(): |
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# Ignore GOs in go2color that are not in the user set |
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if gocolored_cur in go2obj_usr: |
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goobj = go2obj_usr[gocolored_cur] |
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goids_equiv = goobj.alt_ids.union([goobj.id]) |
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# mrk_alt = "*" if gocolored_cur != goobj.id else "" |
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# print("COLORED({}) KEY({}){:1} ALL({})".format( |
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# gocolored_cur, goobj.id, mrk_alt, goids_equiv)) |
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# Loop through GO IDs which are not colored, but are equivalent to colored GO IDs. |
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for goid_add in goids_equiv.difference(gocolored_all): |
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if goid_add in go2color_add: |
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print('**TBD: TWO DIFFERENT COLORS FOR EQUIV GO ID') # pylint: disable=superfluous-parens |
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go2color_add[goid_add] = color |
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# print("ADDING {N} GO IDs TO go2color".format(N=len(go2color_add))) |
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for goid, color in go2color_add.items(): |
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self.go2color[goid] = color |
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# Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved. |
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tanghaibao /
goatools
