from .abstractgene import HOG
import logging
import json
from ete4 import Tree
logger = logging.getLogger(__name__)
[docs]
class TreeProfile(object):
"""
Object that map on each node of the Ham species tree the related evolutionary information such as the number of
genes the related genome contains or the number of evolutionary events (duplications, genes loss or gain of genes)
that occurs between the parent node and itself. This can be either applied to the full Ham comparative genomic setup
or for a specific HOG.
Attributes:
| pyham (:obj:`pyham.pyham.Ham`): :obj:`set` of HOG ids used by the FilterOrthoXMLParser.
| hog (:obj:`pyham.abstractgene.HOG`, optional): If specified, compute TreeProfile on a single HOGs. Defaults is None.
| treemap (:obj:`ete3.Etree`): Ete3 Etree object containing the taxonomy of interest with annotated node.
"""
def __init__(self, ham, hog=None):
self.ham = ham
self.hog = hog
if hog is None:
self.treemap = self.compute_tree_profile_full()
elif isinstance(hog, HOG):
self.treemap = self.computeTP_hog(hog)
else:
raise TypeError("Invalid argument {} for HOG".format(hog))
[docs]
def computeTP_hog(self, hog):
"""
Create the treeMap object (ete3 Etree object with annotated nodes) that contained the following features for
each nodes (representing an AbstractGene):
- nbr_genes: numbers of HOG/Gene the genome contains. For leaves, it also counts the singletons.
- dupl: numbers of HOGs that have arose by duplication in between this node and its parent.
- retained: numbers of HOGs that have stay retained (in term of copy numbers) in between this node and
its parent.
- lost: numbers of HOGs that have been lost in between this node and its parent.
Returns:
TreeMap
"""
# copy the required taxonomy using query hog as root level
treeMap = hog.genome.taxon.copy()
# create a dictionary that map node with related hogs/genes
levelGroups = {}
for lvl in treeMap.traverse():
levelGroups[lvl.name]=[]
# add all of subhog to the related level in levelGroups
for subhog in hog.get_all_descendant_hogs():
if subhog.genome.name in levelGroups:
levelGroups[subhog.genome.name].append(subhog)
# add empty extant genome to levelGroups
for extantGenome in treeMap.leaves():
levelGroups[extantGenome.name] = []
# add genes to related extant genome in levelGroups
for species, genes in hog.get_all_descendant_genes_clustered_by_species().items():
levelGroups[species.name] = genes
for lvl in treeMap.traverse():
lvl.add_prop("nbr_genes", len(levelGroups[lvl.name]))
lvl.add_prop("gain", None)
if not lvl.is_root:
cpt_dupl = 0
cpt_ident = 0
set_dup_parent = set()
for h in levelGroups[lvl.name]:
if h.arose_by_duplication != False:
cpt_dupl += 1
set_dup_parent.add(h.parent)
else:
cpt_ident += 1
cpt_lost = 0
for h_up in levelGroups[lvl.up.name]:
if len(h_up.children) != 0:
found = False
for child in h_up.children:
if child.genome.taxon.name == lvl.name:
found = True
if found is False:
cpt_lost += 1
else:
cpt_lost += 1
cpt_duplication = max(0, cpt_dupl - len(list(set_dup_parent)))
nbr_ev = cpt_lost + cpt_duplication
else:
cpt_dupl = None
cpt_ident = None
cpt_lost = None
cpt_duplication = None
nbr_ev = None
lvl.add_prop("dupl", cpt_dupl)
lvl.add_prop("lost", cpt_lost)
lvl.add_prop("retained", cpt_ident)
lvl.add_prop("nbr_events", nbr_ev)
lvl.add_prop("duplication", cpt_duplication)
return treeMap
[docs]
def compute_tree_profile_full(self):
"""
Create the treeMap object (ete3 Etree object with annotated nodes) that contained the following features for
each nodes (the root node contains only nbr_genes):
- nbr_genes: numbers of HOG/Gene the genome contains. For leaves, it also counts the singletons.
- dupl: numbers of HOGs that have arose by duplication in between this node and its parent.
- lost: numbers of HOGs that have been lost in between this node and its parent.
- gain: numbers of HOGs that have "emerged" at this node.
- retained: numbers of HOGs that have stay retained (in term of copy numbers) in between this node and
its parent.
In order to get all those node informations, the HOGMap between each node and its parent is computed.
Returns:
TreeMap
"""
def _add_annot(node: Tree, nbr, dupl, lost, gain, retained, duplication, nbr_ev):
node.add_prop("nbr_genes", nbr)
node.add_prop("nbr_events", nbr_ev)
node.add_prop("dupl", dupl)
node.add_prop("lost", lost)
node.add_prop("gain", gain)
node.add_prop("retained", retained)
node.add_prop("duplication", duplication)
treeMap = self.ham.taxonomy.tree.copy()
for node in treeMap.traverse():
if node.is_root:
node_genome = self.ham.get_ancestral_genome_by_name(node.name)
_add_annot(node, len(node_genome.genes), None, None, None, None, None, None)
else:
node_genome_up = self.ham._get_ancestral_genome_by_name(node.up.name)
if node.is_leaf:
node_genome = self.ham._get_extant_genome_by_name(name=node.name)
nbr = node_genome.get_number_genes(singleton=True)
else:
node_genome = self.ham._get_ancestral_genome_by_name(node.name)
nbr = node_genome.get_number_genes()
hogmap = self.ham._get_HOGMap({node_genome, node_genome_up})
nbr_duplicate = 0
for gs in hogmap.DUPLICATE.values():
nbr_duplicate += len(gs)
nbr_ev = hogmap.number_duplication + len(hogmap.LOSS) + len(hogmap.GAIN)
_add_annot(node, nbr, nbr_duplicate, len(hogmap.LOSS), len(hogmap.GAIN), len(hogmap.RETAINED.keys()), hogmap.number_duplication, nbr_ev)
return treeMap
[docs]
def export(self, output, layout_function=None, display_internal_histogram=True):
"""
Method to export the tree profile object as figure (available format .SVG, .PDF, .PNG).
-- Some magic going there --
Args:
| output (:obj:`str`): output file name. The extension of output will set the format of the figure (SVG, .PDF, .PNG)
| layout_function (:obj:`function`, optional): custom layout_fn for ete3 TreeStyle.
| display_internal_histogram (:obj:`Boolean`, optional): Display internal node as histogram or raw text with numbers. Defaults to True.
"""
from ete4 import TreeStyle, TextFace, NodeStyle, BarChartFace
# maximum number of genes per node in this treeMap
max_genes = max([d for d in self.treemap.traverse()], key=lambda x:x.nbr_genes).nbr_genes
if self.hog is None:
_color_scheme = ["#41c1c2","#bdc3c7","#f39c12","#27ae60","#e74c3c"]
_label_legend = ["Genes","Retained","Duplicated","Novel","Lost"]
_values_legend = [max_genes,max_genes,max_genes,max_genes,max_genes]
w_legend = 50 # todo calculate base on len(_values)
else:
_color_scheme = ["#41c1c2", "#bdc3c7", "#f39c12", "#e74c3c"]
_label_legend = ["Genes", "Retained", "Duplicated", "Lost"]
_values_legend = [max_genes, max_genes, max_genes, max_genes]
w_legend = 40 # todo calculate base on len(_values)
def _layout(node):
if self.hog is None:
_label = [str(node.nbr_genes),str(node.retained),str(node.dupl),str(node.gain),str(node.lost)]
else:
_label = [str(node.nbr_genes), str(node.retained), str(node.dupl), str(node.lost)]
def _add_face(name_feature, value_feature, cnum=1, pos="branch-right"):
node.add_face(TextFace("{}: {}".format(name_feature, value_feature)), column=cnum, position=pos)
def _add_faces(cNbr=1, posNbr="branch-right", cAttr=2, posAtt="branch-right"):
_add_face("#genes", node.nbr_genes, cnum=cNbr, pos=posNbr)
if node.retained is not None:
_add_face("#Retained", node.retained, cnum=cAttr, pos=posAtt)
if node.dupl is not None:
_add_face("#Duplicated", node.dupl, cnum=cAttr, pos=posAtt)
if node.gain is not None:
_add_face("#Novel", node.gain, cnum=cAttr, pos=posAtt)
if node.lost is not None:
_add_face("#Lost", node.lost, cnum=cAttr, pos=posAtt)
if node.is_leaf:
if display_internal_histogram:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes, node.retained, node.dupl, node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-right")
else:
_add_faces()
else:
if display_internal_histogram:
if node.is_root:
node.add_face(BarChartFace([node.nbr_genes], deviations=None, width=10, height=25, colors=["#41c1c2"], labels=[str(node.nbr_genes)], min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0, position = "branch-bottom")
else:
if self.hog is None:
values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
w_plot = 50
else:
values = [node.nbr_genes,node.retained,node.dupl,node.lost]
w_plot = 40
node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-top")
else:
_add_faces(cNbr=0, posNbr="branch-top", cAttr=0, posAtt="branch-bottom")
ts = TreeStyle()
if layout_function is not None:
ts.layout_fn = layout_function
else:
ts.layout_fn = _layout
ts.legend.add_face(BarChartFace(_values_legend, deviations=None, width=w_legend, height=25, colors=_color_scheme, labels=_label_legend, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0)
ts.legend_position = 3
self.treemap.render(output, tree_style=ts)
[docs]
def export_as_html(self, output):
"""
Method to export the tree profile object as an interactive tool embedded into a html file.
Args:
| output (:obj:`str`): output file name. If filename finish by .html, a double click load the file into your default browser.
"""
def visit_custom(node, data):
current = {
"name": node.props['name'],
"numberGenes": node.props['nbr_genes'],
"numberEvents": node.props['nbr_events'],
"length": 0.01,
"collapsed": "false",
"evolutionaryEvents": {
"retained": None,
"duplicated": None,
"gained": None,
"lost": None,
"duplication": None
}
}
if node.is_root:
current['evolutionaryEvents'] = False
else:
current['evolutionaryEvents']["retained"] = node.props['retained']
current['evolutionaryEvents']["duplicated"] = node.props['dupl']
current['evolutionaryEvents']["gained"] = node.props['gain']
current['evolutionaryEvents']["lost"] = node.props['lost']
current['evolutionaryEvents']["duplication"] = node.props['duplication']
if not node.is_leaf:
current['children'] = []
for child in node.children:
current['children'].append(visit_custom(child, data))
return current
template = '''
<!DOCTYPE html>
<html>
<head>
<title>Phylo.io</title>
<meta charset="UTF-8">
<script src="https://peterolson.github.com/BigInteger.js/BigInteger.min.js"></script>
<script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/jquery-2.1.4.min.js"></script>
<script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/9eae3d2af33f1f75bff78e393909dccfdd400650/www/js/treecompare.js"></script>
<script type="text/javascript" src="https://underscorejs.org/underscore-min.js"></script>
<script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/d3.min.js"></script>
<script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/bootstrap.min.js"></script>
<script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/FileSaver.min.js"></script>
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/solid.css" integrity="sha384-v2Tw72dyUXeU3y4aM2Y0tBJQkGfplr39mxZqlTBDUZAb9BGoC40+rdFCG0m10lXk" crossorigin="anonymous">
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/fontawesome.css" integrity="sha384-q3jl8XQu1OpdLgGFvNRnPdj5VIlCvgsDQTQB6owSOHWlAurxul7f+JpUOVdAiJ5P" crossorigin="anonymous">
<link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/bootstrap-theme.min.css">
<link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/style.css">
<style>
text {{stroke: none;}}
#help_modal_button {{
position: fixed;
right: 10px;
margin-right: 10px; /*magic number */
bottom: 10px;
z-index: 99;
}}
</style>
</head>
<body id="phylo">
<!-- Modal -->
<div class="modal fade bs-example-modal-lg" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>
<h4 class="modal-title" id="myModalLabel">Tree profile help</h4>
</div>
<div class="modal-body">
<embed src="https://cdn.rawgit.com/DessimozLab/pyham/fc01fb94/help.pdf" frameborder="0" width="100%" height="400px">
</div>
<div class="modal-footer">
<button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- Button trigger modal -->
<button id="help_modal_button" type="button" class="btn btn-sm" data-toggle="modal" data-target="#myModal">
Help
</button>
<div id="vis-container1" style="width: 100%; height: 100%;">
<div id="scale-1"> </div>
</div>
<script type="text/javascript">
var treecomp = TreeCompare().init({{
enableScale: true,
scaleColor: "black",
showHistogramValues: true,
showHistogramSummaryValue: true
}});
treeData = '{json_data}';
var tree1 = treecomp.addTree(treeData, undefined, "single");
treecomp.viewTree(tree1.name, "vis-container1", "scale-1");
treecomp.addMainLegend(tree1.name);
</script>
</body>
</html>
'''
data = {}
data = visit_custom(self.treemap, data)
data = json.dumps(data)
template = template.format(json_data=data)
with open(output, 'w') as outfile:
outfile.write(template)