GODagSmallPlot._get_item_str() - Code Metrics - tanghaibao/goatools - Measure and Improve Code Quality continuously with Scrutinizer

GODagSmallPlot._get_item_str() F
last analyzed 2018-07-02 19:48 UTC

↳ Parent: GODagSmallPlot

Complexity

Conditions

Size

Total Lines

Duplication

Lines	23
Ratio	100 %

Importance

Changes

Metric	Value
cc	14
dl	23
loc	23
rs	3.6
c	0
b	0
f	0

How to fix Complexity

"""Plot a GODagSmall."""

__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"

import sys
import os
import collections as cx
from collections import OrderedDict
from goatools.godag_obosm import OboToGoDagSmall

def plot_gos(fout_png, goids, obo_dag, *args, **kws):
    """Given GO ids and the obo_dag, create a plot of paths from GO ids."""
    engine = kws['engine'] if 'engine' in kws else 'pydot'
    godagsmall = OboToGoDagSmall(goids=goids, obodag=obo_dag).godag
    godagplot = GODagSmallPlot(godagsmall, *args, **kws)
    godagplot.plt(fout_png, engine)

def plot_goid2goobj(fout_png, goid2goobj, *args, **kws):
    """Given a dict containing GO id and its goobj, create a plot of paths from GO ids."""
    engine = kws['engine'] if 'engine' in kws else 'pydot'
    godagsmall = OboToGoDagSmall(goid2goobj=goid2goobj).godag
    godagplot = GODagSmallPlot(godagsmall, *args, **kws)
    godagplot.plt(fout_png, engine)

def plot_results(fout_png, goea_results, *args, **kws):
    """Given a list of GOEA results, plot result GOs up to top."""
    if "{NS}" not in fout_png:
        plt_goea_results(fout_png, goea_results, *args, **kws)
    else:
        # Plot separately by NS: BP, MF, CC
        ns2goea_results = cx.defaultdict(list)
        for rec in goea_results:
            ns2goea_results[rec.NS].append(rec)
        for ns_name, ns_res in ns2goea_results.items():
            png = fout_png.format(NS=ns_name)
            plt_goea_results(png, ns_res, *args, **kws)

def plt_goea_results(fout_png, goea_results, *args, **kws):
    """Plot a single page."""
    engine = kws['engine'] if 'engine' in kws else 'pydot'
    godagsmall = OboToGoDagSmall(goea_results=goea_results).godag
    godagplot = GODagSmallPlot(godagsmall, *args, goea_results=goea_results, **kws)
    godagplot.plt(fout_png, engine)

class GODagPltVars(object):
    """Holds plotting paramters."""

    # http://www.graphviz.org/doc/info/colors.html
    rel2col = {
        'is_a':      'black',
        'part_of':   'blue',
        'regulates': 'gold',
        'positively_regulates': 'green',
        'negatively_regulates': 'red',
        'occurs_in':            'aquamarine4',
        'capable_of':           'dodgerblue',
        'capable_of_part_of':   'darkorange',
    }

    alpha2col = OrderedDict([
        # GOEA GO terms that are significant
        (0.005, 'mistyrose'),
        (0.010, 'moccasin'),
        (0.050, 'lemonchiffon1'),
        # GOEA GO terms that are not significant
        (1.000, 'grey95'),
    ])

    key2col = {
        'level_01': 'lightcyan',
        'go_sources': 'palegreen',
    }

    fmthdr = "{GO} L{level:>02} D{depth:>02}"
    fmtres = "{study_count} genes"
    # study items per line on GO Terms:
    items_p_line = 5


class GODagSmallPlot(object):
    """Plot a graph contained in an object of type GODagSmall ."""

    def __init__(self, godagsmall, *args, **kws):
        self.args = args
        self.log = kws['log'] if 'log' in kws else sys.stdout
        self.title = kws['title'] if 'title' in kws else None
        # GOATOOLs results as objects
        self.go2res = self._init_go2res(**kws)
        # GOATOOLs results as a list of namedtuples
        self.pval_name = self._init_pval_name(**kws)
        # Gene Symbol names
        self.id2symbol = kws['id2symbol'] if 'id2symbol' in kws else {}
        self.study_items = kws['study_items'] if 'study_items' in kws else None
        self.study_items_max = self._init_study_items_max()
        self.alpha_str = kws['alpha_str'] if 'alpha_str' in kws else None
        self.pltvars = kws['GODagPltVars'] if 'GODagPltVars' in kws else GODagPltVars()
        if 'items_p_line' in kws:
            self.pltvars.items_p_line = kws['items_p_line']
        self.dpi = kws['dpi'] if 'dpi' in kws else 150
        self.godag = godagsmall
        self.goid2color = self._init_goid2color()
        self.pydot = None

    def _init_study_items_max(self):
        """User can limit the number of genes printed in a GO term."""
        if self.study_items is None:
            return None
        if self.study_items is True:
            return None
        if isinstance(self.study_items, int):
            return self.study_items
        return None

    @staticmethod
    def _init_go2res(**kws):
        """Initialize GOEA results."""
        if 'goea_results' in kws:
            return {res.GO:res for res in kws['goea_results']}
        if 'go2nt' in kws:
            return kws['go2nt']

    @staticmethod
    def _init_pval_name(**kws):
        """Initialize pvalue attribute name."""
        if 'pval_name' in kws:
            return kws['pval_name']
        if 'goea_results' in kws:
            goea = kws['goea_results']
            if goea:
                return "p_{M}".format(M=goea[0].method_flds[0].fieldname)

    def _init_goid2color(self):
        """Set colors of GO terms."""
        goid2color = {}
        # 1. colors based on p-value override colors based on source GO
        if self.go2res is not None:

            alpha2col = self.pltvars.alpha2col
            pval_name = self.pval_name
            for goid, res in self.go2res.items():
                pval = getattr(res, pval_name, None)
                if pval is not None:
                    for alpha, color in alpha2col.items():
                        if pval <= alpha and res.study_count != 0:
                            if goid not in goid2color:
                                goid2color[goid] = color
        # 2. GO source color
        color = self.pltvars.key2col['go_sources']
        for goid in self.godag.go_sources:
            if goid not in goid2color:
                goid2color[goid] = color
        # 3. Level-01 GO color
        color = self.pltvars.key2col['level_01']
        for goid, goobj in self.godag.go2obj.items():
            if goobj.level == 1:
                if goid not in goid2color:
                    goid2color[goid] = color
        return goid2color

    def plt(self, fout_img, engine="pydot"):
        """Plot using pydot, graphviz, or GML."""
        if engine == "pydot":
            self._plt_pydot(fout_img)
        elif engine == "pygraphviz":
            raise Exception("TO BE IMPLEMENTED SOON: ENGINE pygraphvis")
        else:
            raise Exception("UNKNOWN ENGINE({E})".format(E=engine))

    # ----------------------------------------------------------------------------------
    # pydot
    def _plt_pydot(self, fout_img):

        """Plot using the pydot graphics engine."""
        dag = self._get_pydot_graph()
        img_fmt = os.path.splitext(fout_img)[1][1:]
        dag.write(fout_img, format=img_fmt)
        self.log.write("  {GO_USR:>3} usr {GO_ALL:>3} GOs  WROTE: {F}\n".format(
            F=fout_img,
            GO_USR=len(self.godag.go_sources),
            GO_ALL=len(self.godag.go2obj)))

    def _get_pydot_graph(self):
        """Given a DAG, return a pydot digraph object."""
        rel = "is_a"
        pydot = self._get_pydot()
        # Initialize empty dag
        dag = pydot.Dot(label=self.title, graph_type='digraph', dpi="{}".format(self.dpi))
        # Initialize nodes
        go2node = self._get_go2pydotnode()
        # Add nodes to graph
        for node in go2node.values():
            dag.add_node(node)
        # Add edges to graph
        rel2col = self.pltvars.rel2col
        for src, tgt in self.godag.get_edges():
            dag.add_edge(pydot.Edge(
                go2node[tgt], go2node[src],
                shape="normal",
                color=rel2col[rel],
                dir="back")) # invert arrow direction for obo dag convention
        return dag

    def _get_go2pydotnode(self):
        """Create pydot Nodes."""
        go2node = {}
        for goid, goobj in self.godag.go2obj.items():
            txt = self._get_node_text(goid, goobj)
            fillcolor = self.goid2color.get(goid, "white")
            node = self.pydot.Node(
                txt,
                shape="box",
                style="rounded, filled",
                fillcolor=fillcolor,
                color="mediumseagreen")
            go2node[goid] = node
        return go2node

    def _get_pydot(self):
        """Return pydot package. Load pydot, if necessary."""
        if self.pydot:
            return self.pydot
        self.pydot = __import__("pydot")
        return self.pydot

    # ----------------------------------------------------------------------------------
    # Methods for text printed inside GO terms
    def _get_node_text(self, goid, goobj):
        """Return a string to be printed in a GO term box."""
        txt = []
        # Header line: "GO:0036464 L04 D06"
        txt.append(self.pltvars.fmthdr.format(
            GO=goobj.id.replace("GO:", "GO"),
            level=goobj.level,
            depth=goobj.depth))
        # GO name line: "cytoplamic ribonucleoprotein"
        name = goobj.name.replace(",", "\n")
        txt.append(name)
        # study info line: "24 genes"
        study_txt = self._get_study_txt(goid)
        if study_txt is not None:
            txt.append(study_txt)
        # return text string
        return "\n".join(txt)

    def _get_study_txt(self, goid):
        """Get GO text from GOEA study."""
        if self.go2res is not None:
            res = self.go2res.get(goid, None)
            if res is not None:
                if self.study_items is not None:
                    return self._get_item_str(res)
                else:
                    return self.pltvars.fmtres.format(
                        study_count=res.study_count)

    def _get_item_str(self, res):

        """Return genes in any of these formats:
              1. 19264, 17319, 12520, 12043, 74131, 22163, 12575
              2. Ptprc, Mif, Cd81, Bcl2, Sash3, Tnfrsf4, Cdkn1a
              3. 7: Ptprc, Mif, Cd81, Bcl2, Sash3...
        """
        npl = self.pltvars.items_p_line  # Number of items Per Line
        prt_items = sorted([self.__get_genestr(itemid) for itemid in res.study_items])
        prt_multiline = [prt_items[i:i+npl] for i in range(0, len(prt_items), npl)]
        num_items = len(prt_items)
        if self.study_items_max is None:
            genestr = "\n".join([", ".join(str(e) for e in sublist) for sublist in prt_multiline])
            return "{N}) {GENES}".format(N=num_items, GENES=genestr)
        else:
            if num_items <= self.study_items_max:
                strs = [", ".join(str(e) for e in sublist) for sublist in prt_multiline]
                genestr = "\n".join([", ".join(str(e) for e in sublist) for sublist in prt_multiline])
                return genestr
            else:
                short_list = prt_items[:self.study_items_max]
                short_mult = [short_list[i:i+npl] for i in range(0, len(short_list), npl)]
                short_str = "\n".join([", ".join(str(e) for e in sublist) for sublist in short_mult])
                return "".join(["{N} genes; ".format(N=num_items), short_str, "..."])

    def __get_genestr(self, itemid):
        """Given a geneid, return the string geneid or a gene symbol."""
        if self.id2symbol is not None:
            symbol = self.id2symbol.get(itemid, None)
            if symbol is not None:
                return symbol
        if isinstance(itemid, int):
            return str(itemid)
        return itemid

# Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved.


1		"""Plot a GODagSmall."""
2
3		__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
4		__author__ = "DV Klopfenstein"
5
6		import sys
7		import os
8		import collections as cx
9		from collections import OrderedDict
10		from goatools.godag_obosm import OboToGoDagSmall
11
12		def plot_gos(fout_png, goids, obo_dag, args, *kws):
13		"""Given GO ids and the obo_dag, create a plot of paths from GO ids."""
14		engine = kws['engine'] if 'engine' in kws else 'pydot'
15		godagsmall = OboToGoDagSmall(goids=goids, obodag=obo_dag).godag
16		godagplot = GODagSmallPlot(godagsmall, args, *kws)
17		godagplot.plt(fout_png, engine)
18
19		def plot_goid2goobj(fout_png, goid2goobj, args, *kws):
20		"""Given a dict containing GO id and its goobj, create a plot of paths from GO ids."""
21		engine = kws['engine'] if 'engine' in kws else 'pydot'
22		godagsmall = OboToGoDagSmall(goid2goobj=goid2goobj).godag
23		godagplot = GODagSmallPlot(godagsmall, args, *kws)
24		godagplot.plt(fout_png, engine)
25
26		def plot_results(fout_png, goea_results, args, *kws):
27		"""Given a list of GOEA results, plot result GOs up to top."""
28		if "{NS}" not in fout_png:
29		plt_goea_results(fout_png, goea_results, args, *kws)
30		else:
31		# Plot separately by NS: BP, MF, CC
32		ns2goea_results = cx.defaultdict(list)
33		for rec in goea_results:
34		ns2goea_results[rec.NS].append(rec)
35		for ns_name, ns_res in ns2goea_results.items():
36		png = fout_png.format(NS=ns_name)
37		plt_goea_results(png, ns_res, args, *kws)
38
39		def plt_goea_results(fout_png, goea_results, args, *kws):
40		"""Plot a single page."""
41		engine = kws['engine'] if 'engine' in kws else 'pydot'
42		godagsmall = OboToGoDagSmall(goea_results=goea_results).godag
43		godagplot = GODagSmallPlot(godagsmall, args, goea_results=goea_results, *kws)
44		godagplot.plt(fout_png, engine)
45
46		class GODagPltVars(object):
47		"""Holds plotting paramters."""
48
49		# http://www.graphviz.org/doc/info/colors.html
50		rel2col = {
51		'is_a': 'black',
52		'part_of': 'blue',
53		'regulates': 'gold',
54		'positively_regulates': 'green',
55		'negatively_regulates': 'red',
56		'occurs_in': 'aquamarine4',
57		'capable_of': 'dodgerblue',
58		'capable_of_part_of': 'darkorange',
59		}
60
61		alpha2col = OrderedDict([
62		# GOEA GO terms that are significant
63		(0.005, 'mistyrose'),
64		(0.010, 'moccasin'),
65		(0.050, 'lemonchiffon1'),
66		# GOEA GO terms that are not significant
67		(1.000, 'grey95'),
68		])
69
70		key2col = {
71		'level_01': 'lightcyan',
72		'go_sources': 'palegreen',
73		}
74
75		fmthdr = "{GO} L{level:>02} D{depth:>02}"
76		fmtres = "{study_count} genes"
77		# study items per line on GO Terms:
78		items_p_line = 5
79
80
81		class GODagSmallPlot(object):
82		"""Plot a graph contained in an object of type GODagSmall ."""
83
84		def __init__(self, godagsmall, args, *kws):
85		self.args = args
86		self.log = kws['log'] if 'log' in kws else sys.stdout
87		self.title = kws['title'] if 'title' in kws else None
88		# GOATOOLs results as objects
89		self.go2res = self._init_go2res(**kws)
90		# GOATOOLs results as a list of namedtuples
91		self.pval_name = self._init_pval_name(**kws)
92		# Gene Symbol names
93		self.id2symbol = kws['id2symbol'] if 'id2symbol' in kws else {}
94		self.study_items = kws['study_items'] if 'study_items' in kws else None
95		self.study_items_max = self._init_study_items_max()
96		self.alpha_str = kws['alpha_str'] if 'alpha_str' in kws else None
97		self.pltvars = kws['GODagPltVars'] if 'GODagPltVars' in kws else GODagPltVars()
98		if 'items_p_line' in kws:
99		self.pltvars.items_p_line = kws['items_p_line']
100		self.dpi = kws['dpi'] if 'dpi' in kws else 150
101		self.godag = godagsmall
102		self.goid2color = self._init_goid2color()
103		self.pydot = None
104
105		def _init_study_items_max(self):
106		"""User can limit the number of genes printed in a GO term."""
107		if self.study_items is None:
108		return None
109		if self.study_items is True:
110		return None
111		if isinstance(self.study_items, int):
112		return self.study_items
113		return None
114
115		@staticmethod
116		def _init_go2res(**kws):
117		"""Initialize GOEA results."""
118		if 'goea_results' in kws:
119		return {res.GO:res for res in kws['goea_results']}
120		if 'go2nt' in kws:
121		return kws['go2nt']
122
123		@staticmethod
124		def _init_pval_name(**kws):
125		"""Initialize pvalue attribute name."""
126		if 'pval_name' in kws:
127		return kws['pval_name']
128		if 'goea_results' in kws:
129		goea = kws['goea_results']
130		if goea:
131		return "p_{M}".format(M=goea[0].method_flds[0].fieldname)
132
133		def _init_goid2color(self):
134		"""Set colors of GO terms."""
135		goid2color = {}
136		# 1. colors based on p-value override colors based on source GO
137	View Code Duplication	if self.go2res is not None:
		0 ignored issues – show Duplication introduced 2018-06-15 18:48 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
138		alpha2col = self.pltvars.alpha2col
139		pval_name = self.pval_name
140		for goid, res in self.go2res.items():
141		pval = getattr(res, pval_name, None)
142		if pval is not None:
143		for alpha, color in alpha2col.items():
144		if pval <= alpha and res.study_count != 0:
145		if goid not in goid2color:
146		goid2color[goid] = color
147		# 2. GO source color
148		color = self.pltvars.key2col['go_sources']
149		for goid in self.godag.go_sources:
150		if goid not in goid2color:
151		goid2color[goid] = color
152		# 3. Level-01 GO color
153		color = self.pltvars.key2col['level_01']
154		for goid, goobj in self.godag.go2obj.items():
155		if goobj.level == 1:
156		if goid not in goid2color:
157		goid2color[goid] = color
158		return goid2color
159
160		def plt(self, fout_img, engine="pydot"):
161		"""Plot using pydot, graphviz, or GML."""
162		if engine == "pydot":
163		self._plt_pydot(fout_img)
164		elif engine == "pygraphviz":
165		raise Exception("TO BE IMPLEMENTED SOON: ENGINE pygraphvis")
166		else:
167		raise Exception("UNKNOWN ENGINE({E})".format(E=engine))
168
169		# ----------------------------------------------------------------------------------
170		# pydot
171	View Code Duplication	def _plt_pydot(self, fout_img):
		0 ignored issues – show Duplication introduced 2018-06-15 18:48 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
172		"""Plot using the pydot graphics engine."""
173		dag = self._get_pydot_graph()
174		img_fmt = os.path.splitext(fout_img)[1][1:]
175		dag.write(fout_img, format=img_fmt)
176		self.log.write(" {GO_USR:>3} usr {GO_ALL:>3} GOs WROTE: {F}\n".format(
177		F=fout_img,
178		GO_USR=len(self.godag.go_sources),
179		GO_ALL=len(self.godag.go2obj)))
180
181		def _get_pydot_graph(self):
182		"""Given a DAG, return a pydot digraph object."""
183		rel = "is_a"
184		pydot = self._get_pydot()
185		# Initialize empty dag
186		dag = pydot.Dot(label=self.title, graph_type='digraph', dpi="{}".format(self.dpi))
187		# Initialize nodes
188		go2node = self._get_go2pydotnode()
189		# Add nodes to graph
190		for node in go2node.values():
191		dag.add_node(node)
192		# Add edges to graph
193		rel2col = self.pltvars.rel2col
194		for src, tgt in self.godag.get_edges():
195		dag.add_edge(pydot.Edge(
196		go2node[tgt], go2node[src],
197		shape="normal",
198		color=rel2col[rel],
199		dir="back")) # invert arrow direction for obo dag convention
200		return dag
201
202		def _get_go2pydotnode(self):
203		"""Create pydot Nodes."""
204		go2node = {}
205		for goid, goobj in self.godag.go2obj.items():
206		txt = self._get_node_text(goid, goobj)
207		fillcolor = self.goid2color.get(goid, "white")
208		node = self.pydot.Node(
209		txt,
210		shape="box",
211		style="rounded, filled",
212		fillcolor=fillcolor,
213		color="mediumseagreen")
214		go2node[goid] = node
215		return go2node
216
217		def _get_pydot(self):
218		"""Return pydot package. Load pydot, if necessary."""
219		if self.pydot:
220		return self.pydot
221		self.pydot = __import__("pydot")
222		return self.pydot
223
224		# ----------------------------------------------------------------------------------
225		# Methods for text printed inside GO terms
226		def _get_node_text(self, goid, goobj):
227		"""Return a string to be printed in a GO term box."""
228		txt = []
229		# Header line: "GO:0036464 L04 D06"
230		txt.append(self.pltvars.fmthdr.format(
231		GO=goobj.id.replace("GO:", "GO"),
232		level=goobj.level,
233		depth=goobj.depth))
234		# GO name line: "cytoplamic ribonucleoprotein"
235		name = goobj.name.replace(",", "\n")
236		txt.append(name)
237		# study info line: "24 genes"
238		study_txt = self._get_study_txt(goid)
239		if study_txt is not None:
240		txt.append(study_txt)
241		# return text string
242		return "\n".join(txt)
243
244		def _get_study_txt(self, goid):
245		"""Get GO text from GOEA study."""
246		if self.go2res is not None:
247		res = self.go2res.get(goid, None)
248		if res is not None:
249		if self.study_items is not None:
250		return self._get_item_str(res)
251		else:
252		return self.pltvars.fmtres.format(
253		study_count=res.study_count)
254
255	View Code Duplication	def _get_item_str(self, res):
		0 ignored issues – show Duplication introduced 2018-06-15 18:48 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
256		"""Return genes in any of these formats:
257		1. 19264, 17319, 12520, 12043, 74131, 22163, 12575
258		2. Ptprc, Mif, Cd81, Bcl2, Sash3, Tnfrsf4, Cdkn1a
259		3. 7: Ptprc, Mif, Cd81, Bcl2, Sash3...
260		"""
261		npl = self.pltvars.items_p_line # Number of items Per Line
262		prt_items = sorted([self.__get_genestr(itemid) for itemid in res.study_items])
263		prt_multiline = [prt_items[i:i+npl] for i in range(0, len(prt_items), npl)]
264		num_items = len(prt_items)
265		if self.study_items_max is None:
266		genestr = "\n".join([", ".join(str(e) for e in sublist) for sublist in prt_multiline])
267		return "{N}) {GENES}".format(N=num_items, GENES=genestr)
268		else:
269		if num_items <= self.study_items_max:
270		strs = [", ".join(str(e) for e in sublist) for sublist in prt_multiline]
271		genestr = "\n".join([", ".join(str(e) for e in sublist) for sublist in prt_multiline])
272		return genestr
273		else:
274		short_list = prt_items[:self.study_items_max]
275		short_mult = [short_list[i:i+npl] for i in range(0, len(short_list), npl)]
276		short_str = "\n".join([", ".join(str(e) for e in sublist) for sublist in short_mult])
277		return "".join(["{N} genes; ".format(N=num_items), short_str, "..."])
278
279		def __get_genestr(self, itemid):
280		"""Given a geneid, return the string geneid or a gene symbol."""
281		if self.id2symbol is not None:
282		symbol = self.id2symbol.get(itemid, None)
283		if symbol is not None:
284		return symbol
285		if isinstance(itemid, int):
286		return str(itemid)
287		return itemid
288
289		# Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved.
290

tanghaibao / goatools

GODagSmallPlot._get_item_str() F last analyzed 2018-07-02 19:48 UTC

Complexity

Size

Duplication

Importance

How to fix Complexity

Complexity

Duplication Side-by-Side

Filter issues like

GODagSmallPlot._get_item_str() F
last analyzed 2018-07-02 19:48 UTC