def my_layout(node):
if getattr(node, "rank", None):
rank_face = AttrFace("rank", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
def layout(node):
if node.is_leaf():
#######################################################
#~ Taxon Label Size and Margin Adjustment
N = AttrFace("name", fsize=1200,fgcolor="#000000")
N.margin_top = 250
N.margin_right = 100 #outside
N.margin_left = 1000 #inside
N.margin_bottom = 250
#######################################################
#######################################################
#~ Taxon Label Background Color Setting
tmp = "<myTaxaonLabel>"
#~ if not(node.name.find(tmp)) : N.background.color="#FF9999"
#######################################################
faces.add_face_to_node(N, node, 0, position="aligned")
if (not node.is_leaf()) :
S=faces.AttrFace("support", fsize=200, fgcolor="#000000")
S.margin_top = 20
S.margin_right = 10
S.margin_left = 20
S.margin_bottom = 20
faces.add_face_to_node( S, node, column=0 , position = "float")
if "support" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.support*20, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, position="float",column=1)
style = NodeStyle()
style["size"] = 0
style["vt_line_width"] = 150
style["hz_line_width"] = 150
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
bgcol1="#FFCCCC"
bgcol2="#FFE5CC"
bgcol3="#FFFFCC"
bgcol4="#E5FFCC"
bgcol5="#CCFFCC"
bgcol6="#CCFFE5"
bgcol7="#FFCCE5"
bgcol8="#CCFFFF"
bgcol9="#CCE5FF"
bgcol10="#CCCCFF"
bgcol11="#E5CCFF"
def layout(node):
if node.up is not None:
attr = AttrFace("expansion", fsize=7, fgcolor="green", text_prefix="+")
faces.add_face_to_node(attr, node, 0, position="branch-top")
attr = AttrFace("decrease", fsize=7, fgcolor="red", text_prefix="-")
faces.add_face_to_node(attr, node, 0, position="branch-bottom")
if node.is_leaf():
attr = AttrFace("name",
fsize=10,
fgcolor="black",
text_prefix=" ",
fstyle="italic")
faces.add_face_to_node(attr, node, 0, position="aligned")
def layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if (node.rank in ['order', 'class', 'phylum', 'kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name == 'annotation':
s = str(msa_dict[str(taxid2gi[int(node.name)])])
seqFace = SeqMotifFace(
s, [[0, len(s), "seq", 10, 10, None, None, None]],
scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
gi = taxid2gi[int(node.name)]
add_face_to_node(TextFace(' ' + str(gi) + ' '),
node,
column=1,
position="aligned")
add_face_to_node(TextFace(' ' + str(int(node.name)) + ' '),
node,
column=2,
position="aligned")
add_face_to_node(TextFace(' ' + str(gi2variant[gi]) + ' '),
node,
column=3,
position="aligned")
if node.is_leaf() and node.name == 'annotation':
s = get_hist_ss_in_aln_as_string(msa_tr)
seqFace = SeqMotifFace(
s, [[0, len(s), "seq", 10, 10, None, None, None]],
scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
add_face_to_node(TextFace(' ' + 'NCBI_GI' + ' '),
node,
column=1,
position="aligned")
add_face_to_node(TextFace(' ' + 'NCBI_TAXID' + ' '),
node,
column=2,
position="aligned")
add_face_to_node(TextFace(' ' + 'Variant' + ' '),
node,
column=3,
position="aligned")
def layout(node):
#print(node)
if node.is_leaf():
if node.name in x_file_names:
#make reconstructed bubble
size = x[x_file_names.index(node.name)]
F = CircleFace(radius=500 * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
if taxonomic_names_on_leaves:
nameFace = AttrFace(
"name",
fsize=25,
fgcolor='black',
text_suffix="_" +
taxonomy[x_file_names.index(node.name)])
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
else:
nameFace = AttrFace("name", fsize=25, fgcolor='black')
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in x_file_names:
idx = hyp_node_names[node.name][2]
size = x[x_file_names.index(node_base_name) +
(idx + 1) * len(x_file_names)]
F = CircleFace(radius=500 * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#print node
#print size
else:
size = 0
else:
size = 0
def print_colored_host_tree(host_tree_fp, host_colors, output_fp, treefmt=5):
with open(host_tree_fp) as tree_f:
treestring = remove_newick_node_labels(tree_f.readline().strip())
tree = Tree(newick=treestring, format=treefmt)
for host in host_colors:
if tree.get_leaves_by_name(host) == []:
tip = "'%s'" % host
else:
tip = host
node = tree.get_leaves_by_name(tip)[0]
node.add_face(AttrFace("name", fsize=14, fgcolor=host_colors[host]), 0)
# remove stupid blue circles on nodes
style = NodeStyle()
style["size"] = 0
for l in tree.traverse():
l.set_style(style)
# get rid of default rendered leaf labels
ts = TreeStyle()
ts.show_leaf_name = False
tree.render(output_fp, tree_style=ts)
return
def print_colored_host_tree(host_tree_fp, host_colors, output_fp):
tree = Tree(host_tree_fp)
for host in host_colors:
if tree.get_leaves_by_name(host) == []:
tip = "'%s'" % host
else:
tip = host
node = tree.get_leaves_by_name(tip)[0]
node.add_face(AttrFace("name", fsize=14, fgcolor=host_colors[host]), 0)
# remove stupid blue circles on nodes
style = NodeStyle()
style["size"] = 0
for l in tree.traverse():
l.set_style(style)
# get rid of default rendered leaf labels
ts = TreeStyle()
ts.show_leaf_name = False
tree.render(output_fp, tree_style=ts)
return
def my_layout(node):
from ete2 import AttrFace, faces
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0, position="aligned")
else:
node.img_style["size"] = 0
node.img_style["fgcolor"] = "#000000"
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=7)
faces.add_face_to_node(faces.AttrFace("name", "Arial", 10, None),
node,
0,
position='branch-right')
def my_layout(node):
if node.name != "43":
print node.name
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("species", fsize=16)
pie = PieChartFace([changes[node.name][0], changes[node.name][1]],
changes[node.name][2], changes[node.name][2],
["Green", "Red"])
pie.opacity = 0.5
#name_face = AttrFace("name", fsize=16)
faces.add_face_to_node(name_face,
node,
column=0,
position="branch-right")
faces.add_face_to_node(pie, node, column=0, position="float")
else:
# If internal node, draws label with smaller font size
#name_face = AttrFace("name", fsize=10)
pie = PieChartFace([changes[node.name][0], changes[node.name][1]],
changes[node.name][2], changes[node.name][2],
["Green", "Red"])
pie.opacity = 0.5
#faces.add_face_to_node(name_face, node, column=0, position="branch-right")
faces.add_face_to_node(pie, node, column=0, position="float")
def layout_simple(node):
if node.is_leaf():
attr = AttrFace("name",
fsize=10,
fgcolor="black",
text_prefix=" ",
fstyle="italic")
faces.add_face_to_node(attr, node, 0, position="aligned")
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
small_tree = small_d[node.name]
T = TreeFace(small_tree, small_ts)
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def layout(node):
if node.is_leaf():
#######################################################
#~ Taxon Label Size and Margin Adjustment
N = AttrFace("name", fsize=1200, fgcolor="#000000")
N.margin_top = 250
N.margin_right = 100 #outside
N.margin_left = 1000 #inside
N.margin_bottom = 250
#######################################################
#######################################################
#~ Taxon Label Background Color Setting
tmp = "<myTaxaonLabel>"
#~ if not(node.name.find(tmp)) : N.background.color="#FF9999"
#######################################################
faces.add_face_to_node(N, node, 0, position="aligned")
if (not node.is_leaf()):
S = faces.AttrFace("support", fsize=200, fgcolor="#000000")
S.margin_top = 20
S.margin_right = 10
S.margin_left = 20
S.margin_bottom = 20
faces.add_face_to_node(S, node, column=0, position="float")
if "support" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.support * 20,
color="RoyalBlue",
style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, position="float", column=1)
style = NodeStyle()
style["size"] = 0
style["vt_line_width"] = 150
style["hz_line_width"] = 150
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
bgcol1 = "#FFCCCC"
bgcol2 = "#FFE5CC"
bgcol3 = "#FFFFCC"
bgcol4 = "#E5FFCC"
bgcol5 = "#CCFFCC"
bgcol6 = "#CCFFE5"
bgcol7 = "#FFCCE5"
bgcol8 = "#CCFFFF"
bgcol9 = "#CCE5FF"
bgcol10 = "#CCCCFF"
bgcol11 = "#E5CCFF"
def my_layout(node):
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
# style2["vt_line_color"] = "#0000aa"
# style2["hz_line_color"] = "#0000aa"
# style2["vt_line_width"] = 2
# style2["hz_line_width"] = 2
# style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
# style2["hz_line_type"] = 1
node.img_style = style2
node.img_style["bgcolor"] = "LightSteelBlue"
if node.is_leaf():
# If terminal node, draws its name
# name_faces = AttrFace("name")
node.img_style["size"] = 40
# node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#FFFFFF"
# node.img_style["fgcolor"] = "#9db0cf"
# node.img_style["bgcolor"] = "#9db0cf"
# node.img_style["faces_bgcolor"] = "#9db0cf"
# node.img_style["bgcolor"] = "#9db0cf"
# node.img_style["bgcolor"] = "#9db0cf"
pass
else:
# If internal node, draws label with smaller font size
# name_faces = AttrFace("name", fsize=15)
# Adds the name face to the image at the preferred position
# faces.add_face_to_node(name_faces, node, column=0, position="branch-top")
# tempo = faces.ImgFace(plot_folder + "/" + node.name + '.jpg')
# faces.add_face_to_node(tempo, node, column=0, position="branch-bottom")
node.img_style["size"] = 40
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#FFFFFF"
tempt = AttrFace('name', fsize=80)
tempt.fgcolor = "Black"
tempt.margin_top = 10
tempt.margin_right = 10
tempt.margin_left = 10
tempt.margin_bottom = 10
tempt.opacity = 0.5 # from 0 to 1
tempt.inner_border.width = 1 # 1 pixel border
tempt.inner_border.type = 1 # dashed line
tempt.border.width = 1
# tempt.background.color = "LightGreen"
# tempt.penwidth = 40
node.add_face(tempt, column=0, position="branch-top")
def layout(node):
node_style = NodeStyle()
node_style["hz_line_width"] = 10
node_style["vt_line_width"] = 10
node.set_style(node_style)
#print(node)
if node.is_leaf():
if node.name in org_names:
#make reconstructed bubble
size = x[org_names.index(node.name)]
F = CircleFace(radius=size_factor * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#Denote that this was a training organism
nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
faces.add_face_to_node(nameFace,
node,
0,
position="branch-right")
elif node.name in hyp_node_names: #Otherwise it's a hypothetical node, just use recon x
node_base_name = hyp_node_names[node.name][0]
percent = hyp_node_names[node.name][1]
if node_base_name in org_names:
idx = hyp_node_names[node.name][2]
size = x[org_names.index(node_base_name) +
(idx + 1) * len(org_names)]
F = CircleFace(radius=size_factor * math.sqrt(size),
color="RoyalBlue",
style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="branch-right")
#This is if I want the names of the hypothetical nodes to be printed as well
#nameFace = AttrFace("name", fsize=font_size, fgcolor='black')
#faces.add_face_to_node(nameFace, node, 0, position="branch-right")
else:
size = 0
else:
size = 0
def __layout__(self, node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
nstyle = NodeStyle()
nstyle["size"] = 0
node.set_style(nstyle)
if "internalCount" in node.features:
print node.name
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=int(node.internalCount) / 10,
color="RoyalBlue",
style="sphere")
T = TextFace("10")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
faces.add_face_to_node(T, node, 1)
def layout(node):
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=14, fgcolor=node.tip_color)
faces.add_face_to_node(N, node, 0)
def layout(node, feature):
if node.up is not None or feature == "id":
attr = AttrFace(feature, fsize=5, fgcolor="green")
faces.add_face_to_node(attr, node, 0, position="branch-top")
def draw_tree(tree, conf, outfile):
try:
from ete2 import (add_face_to_node, AttrFace, TextFace, TreeStyle,
RectFace, CircleFace, SequenceFace, random_color,
SeqMotifFace)
except ImportError as e:
print e
return
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt",
fsize=6,
fgcolor='#444',
ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species,
fsize=10,
fgcolor='#444444',
fstyle='italic',
ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" % node.genename,
fsize=8,
fgcolor='#777777',
ftype='Helvetica')
add_face_to_node(geneF,
node,
column=1,
position='branch-right')
def ly_supports(node):
if not node.is_leaf() and node.up:
supFace = TextFace("%0.2g" % (node.support),
fsize=7,
fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly_tax_labels(node):
if node.is_leaf():
c = LABEL_START_COL
largest = 0
for tname in TRACKED_CLADES:
if hasattr(node,
"named_lineage") and tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.margin_right = 2
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
node,
c,
position='aligned')
c += 1
def ly_full_alg(node):
pass
def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c + 1 == len(node.sequence):
start, end = last_lt, c
motifs.append([
start, end, "()", 0, 12, "slategrey",
"slategrey", None
])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c - 1
motifs.append([
start, end, "()", 0, 12, "grey", "slategrey",
None
])
last_lt = None
seqFace = SeqMotifFace(node.sequence,
motifs,
intermotif_format="line",
seqtail_format="line",
scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
TRACKED_CLADES = [
"Eukaryota",
"Viridiplantae",
"Fungi",
"Alveolata",
"Metazoa",
"Stramenopiles",
"Rhodophyta",
"Amoebozoa",
"Crypthophyta",
"Bacteria",
"Alphaproteobacteria",
"Betaproteobacteria",
"Cyanobacteria",
"Gammaproteobacteria",
]
# ["Opisthokonta", "Apicomplexa"]
colors = random_color(num=len(TRACKED_CLADES), s=0.45)
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])
NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')
LABEL_START_COL = 10
ALG_START_COL = 40
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.scale = 160
ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]
MIXED_RES = set()
MAX_SEQ_LEN = 0
NPR_TREES = []
for n in tree.traverse():
if hasattr(n, "tree_seqtype"):
MIXED_RES.add(n.tree_seqtype)
if hasattr(n, "tree_type"):
NPR_TREES.append(n.tree_type)
seq = getattr(n, "sequence", "")
MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)
if MAX_SEQ_LEN:
ALG_SCALE = min(1, 1000. / MAX_SEQ_LEN)
ts.layout_fn.append(ly_block_alg)
if len(NPR_TREES) > 1:
rF = RectFace(4, 4, "steelblue", "steelblue")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" NPR node"), 1)
ts.legend_position = 3
if len(MIXED_RES) > 1:
rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
ts.legend_position = 3
try:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
a = tree.search_nodes(species='Dictyostelium discoideum')[0]
b = tree.search_nodes(species='Chondrus crispus')[0]
#out = tree.get_common_ancestor([a, b])
#out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
tree.set_outgroup(out)
tree.swap_children()
except Exception:
pass
tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile + '.svg', tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile + '.pdf', tree_style=ts, w=170, units='mm', dpi=150)
def createLineageTrees(self, fn=None, width=None, height=None, circular=False, withAppearing=True, from_t=0, to_t=0):
from ete2 import Tree, NodeStyle, AttrFace
tree = Tree()
style = self.getNodeStyle()
divisionStyle = self.getNodeStyle()
invisibleNodeStyle = NodeStyle()
invisibleNodeStyle["hz_line_color"] = "white"
invisibleNodeStyle["vt_line_color"] = "white"
invisibleNodeStyle["fgcolor"] = "white"
distanceFromRoot = 0
nodeMap = {}
branchSize = {}
# add all nodes which appear in the first frame
for event in self.mainOperator.innerOperators[0].events[from_t]:
if event.type != pgmlink.EventType.Appearance:
label = event.traxel_ids[0]
appNode = tree.add_child(name=self.getNodeName(0, label), dist=distanceFromRoot )
nodeMap[str(self.getNodeName(0, label))] = appNode
branchSize[str(self.getNodeName(0, label))] = 0
# making the branches to the root node invisible
n = appNode
while n:
n.set_style(invisibleNodeStyle)
n = n.up
appNode.set_style(invisibleNodeStyle)
name = AttrFace("name")
name.fsize = 6
# add all lineages
for t, events_at in enumerate(self.mainOperator.innerOperators[0].events[from_t:to_t+1]):
t = t+1
for event in events_at:
if event.type == pgmlink.EventType.Appearance and withAppearing:
label = event.traxel_ids[0]
appNode = tree.add_child(name=self.getNodeName(t, label), dist=distanceFromRoot + t)
nodeMap[str(self.getNodeName(t, label))] = appNode
branchSize[str(self.getNodeName(t, label))] = 0
# making the branches to the root node invisible
n = appNode
while n:
n.set_style(invisibleNodeStyle)
n = n.up
appNode.set_style(invisibleNodeStyle)
name = AttrFace("name")
name.fsize = 6
elif event.type == pgmlink.EventType.Disappearance:
label = event.traxel_ids[0]
if str(self.getNodeName(t-1,str(label))) not in nodeMap.keys():
continue
if branchSize[str(self.getNodeName(t-1,str(label)))] == 0:
del nodeMap[str(self.getNodeName(t-1,str(label)))]
del branchSize[str(self.getNodeName(t-1,str(label)))]
continue
newNode = nodeMap[str(self.getNodeName(t-1,str(label)))].add_child(
name = self.getNodeName(t-1,str(label)),dist = branchSize[str(self.getNodeName(t-1,str(label)))])
newNode.set_style(style)
del nodeMap[str(self.getNodeName(t-1,str(label)))]
del branchSize[str(self.getNodeName(t-1,str(label)))]
elif event.type == pgmlink.EventType.Division:
labelOld = event.traxel_ids[0]
labelNew1 = event.traxel_ids[1]
labelNew2 = event.traxel_ids[2]
if str(self.getNodeName(t-1,str(labelOld))) not in nodeMap.keys():
continue
newNode = nodeMap[str(self.getNodeName(t-1,str(labelOld)))].add_child(
name = self.getNodeName(t-1,str(self.getNodeName(t-1,str(labelOld)))),
dist = branchSize[str(self.getNodeName(t-1,str(labelOld)))] )
del nodeMap[str(self.getNodeName(t-1,str(labelOld)))]
del branchSize[str(self.getNodeName(t-1,str(labelOld)))]
newNode.set_style(divisionStyle)
nodeMap[str(self.getNodeName(t,str(labelNew1)))] = newNode
nodeMap[str(self.getNodeName(t,str(labelNew2)))] = newNode
branchSize[str(self.getNodeName(t,str(labelNew1)))] = 1
branchSize[str(self.getNodeName(t,str(labelNew2)))] = 1
elif event.type == pgmlink.EventType.Move:
labelOld = event.traxel_ids[0]
labelNew = event.traxel_ids[1]
if str(self.getNodeName(t-1,str(labelOld))) not in nodeMap.keys():
continue
nodeMap[str(self.getNodeName(t,str(labelNew)))] = nodeMap[str(self.getNodeName(t-1,str(labelOld)))]
del nodeMap[str(self.getNodeName(t-1,str(labelOld)))]
branchSize[str(self.getNodeName(t,str(labelNew)))] = branchSize[str(self.getNodeName(t-1,str(labelOld)))] + 1
del branchSize[str(self.getNodeName(t-1,str(labelOld)))]
else:
raise Exception, "lineage tree generation not implemented for event type " + str(event.type)
for label in nodeMap.keys():
newNode = nodeMap[label].add_child(name = label,dist = branchSize[label])
self.plotTree(tree, out_fn=fn, rotation=270, show_leaf_name=False,
show_branch_length=False, circularTree=circular, show_division_nodes=False,
distance_between_branches=4, width=width, height=height)
def createLineageTrees(self,
fn=None,
width=None,
height=None,
circular=False,
withAppearing=True,
from_t=0,
to_t=0):
from ete2 import Tree, NodeStyle, AttrFace
tree = Tree()
style = self.getNodeStyle()
divisionStyle = self.getNodeStyle()
invisibleNodeStyle = NodeStyle()
invisibleNodeStyle["hz_line_color"] = "white"
invisibleNodeStyle["vt_line_color"] = "white"
invisibleNodeStyle["fgcolor"] = "white"
distanceFromRoot = 0
nodeMap = {}
branchSize = {}
# add all nodes which appear in the first frame
for event in self.mainOperator.innerOperators[0].events[from_t]:
if event.type != pgmlink.EventType.Appearance:
label = event.traxel_ids[0]
appNode = tree.add_child(name=self.getNodeName(0, label),
dist=distanceFromRoot)
nodeMap[str(self.getNodeName(0, label))] = appNode
branchSize[str(self.getNodeName(0, label))] = 0
# making the branches to the root node invisible
n = appNode
while n:
n.set_style(invisibleNodeStyle)
n = n.up
appNode.set_style(invisibleNodeStyle)
name = AttrFace("name")
name.fsize = 6
# add all lineages
for t, events_at in enumerate(
self.mainOperator.innerOperators[0].events[from_t:to_t + 1]):
t = t + 1
for event in events_at:
if event.type == pgmlink.EventType.Appearance and withAppearing:
label = event.traxel_ids[0]
appNode = tree.add_child(name=self.getNodeName(t, label),
dist=distanceFromRoot + t)
nodeMap[str(self.getNodeName(t, label))] = appNode
branchSize[str(self.getNodeName(t, label))] = 0
# making the branches to the root node invisible
n = appNode
while n:
n.set_style(invisibleNodeStyle)
n = n.up
appNode.set_style(invisibleNodeStyle)
name = AttrFace("name")
name.fsize = 6
elif event.type == pgmlink.EventType.Disappearance:
label = event.traxel_ids[0]
if str(self.getNodeName(t - 1,
str(label))) not in nodeMap.keys():
continue
if branchSize[str(self.getNodeName(t - 1,
str(label)))] == 0:
del nodeMap[str(self.getNodeName(t - 1, str(label)))]
del branchSize[str(self.getNodeName(t - 1,
str(label)))]
continue
newNode = nodeMap[str(self.getNodeName(
t - 1, str(label)))].add_child(
name=self.getNodeName(t - 1, str(label)),
dist=branchSize[str(
self.getNodeName(t - 1, str(label)))])
newNode.set_style(style)
del nodeMap[str(self.getNodeName(t - 1, str(label)))]
del branchSize[str(self.getNodeName(t - 1, str(label)))]
elif event.type == pgmlink.EventType.Division:
labelOld = event.traxel_ids[0]
labelNew1 = event.traxel_ids[1]
labelNew2 = event.traxel_ids[2]
if str(self.getNodeName(
t - 1, str(labelOld))) not in nodeMap.keys():
continue
newNode = nodeMap[str(
self.getNodeName(t - 1, str(labelOld)))].add_child(
name=self.getNodeName(
t - 1,
str(self.getNodeName(t - 1, str(labelOld)))),
dist=branchSize[str(
self.getNodeName(t - 1, str(labelOld)))])
del nodeMap[str(self.getNodeName(t - 1, str(labelOld)))]
del branchSize[str(self.getNodeName(t - 1, str(labelOld)))]
newNode.set_style(divisionStyle)
nodeMap[str(self.getNodeName(t, str(labelNew1)))] = newNode
nodeMap[str(self.getNodeName(t, str(labelNew2)))] = newNode
branchSize[str(self.getNodeName(t, str(labelNew1)))] = 1
branchSize[str(self.getNodeName(t, str(labelNew2)))] = 1
elif event.type == pgmlink.EventType.Move:
labelOld = event.traxel_ids[0]
labelNew = event.traxel_ids[1]
if str(self.getNodeName(
t - 1, str(labelOld))) not in nodeMap.keys():
continue
nodeMap[str(self.getNodeName(
t, str(labelNew)))] = nodeMap[str(
self.getNodeName(t - 1, str(labelOld)))]
del nodeMap[str(self.getNodeName(t - 1, str(labelOld)))]
branchSize[str(self.getNodeName(
t, str(labelNew)))] = branchSize[str(
self.getNodeName(t - 1, str(labelOld)))] + 1
del branchSize[str(self.getNodeName(t - 1, str(labelOld)))]
else:
raise Exception, "lineage tree generation not implemented for event type " + str(
event.type)
for label in nodeMap.keys():
newNode = nodeMap[label].add_child(name=label,
dist=branchSize[label])
self.plotTree(tree,
out_fn=fn,
rotation=270,
show_leaf_name=False,
show_branch_length=False,
circularTree=circular,
show_division_nodes=False,
distance_between_branches=4,
width=width,
height=height)
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 70, "cbars")
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
print node
print node.silhouette
def my_layout(node):
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
node.img_style = style2
node.img_style["bgcolor"] = "LightSteelBlue"
if node.is_leaf():
node.img_style["size"] = 40
node.img_style["fgcolor"] = "#FFFFFF"
pass
else:
node.img_style["size"] = 40
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#FFFFFF"
tempt = AttrFace('name', fsize=80)
tempt.fgcolor = "Black"
tempt.margin_top = 10
tempt.margin_right = 10
tempt.margin_left = 10
tempt.margin_bottom = 10
tempt.opacity = 0.5 # from 0 to 1
tempt.inner_border.width = 1 # 1 pixel border
tempt.inner_border.type = 1 # dashed line
tempt.border.width = 1
node.add_face(tempt, column=0, position="branch-top")
tempt = AttrFace('alias', fsize=80)
tempt.fgcolor = "Black"
tempt.margin_top = 10
tempt.margin_right = 10
tempt.margin_left = 10
tempt.margin_bottom = 10
tempt.opacity = 0.5 # from 0 to 1
tempt.inner_border.width = 1 # 1 pixel border
tempt.inner_border.type = 1 # dashed line
tempt.border.width = 1
node.add_face(tempt, column=0, position="branch-bottom")
def plot_heat_tree(heatmap_file, tree_file, output_file=None):
'''
Plot heatmap next to a tree. The order of the heatmap **MUST** be the same,
as order of the leafs on the tree. The tree must be in the Newick format. If
*output_file* is specified, then heat-tree will be rendered as a PNG,
otherwise interactive browser will pop-up with your heat-tree.
Parameters
----------
heatmap_file: str
Path to the heatmap file. The first row must have '#Names' as first
element of the header.
e.g. #Names, A, B, C, D
row1, 2, 4, 0, 4
row2, 4, 6, 2, -1
tree_file: str
Path to the tree file in Newick format. The leaf node labels should
be the same as as row names in the heatmap file. E.g. row1, row2.
output_file: str, optional
If specified the heat-tree will be rendered in that file as a PNG image,
otherwise interactive browser will pop-up. **N.B.** program will wait
for you to exit the browser before continuing.
'''
import numpy
from ete2.treeview.faces import add_face_to_node
from ete2 import ClusterTree, TreeStyle, AttrFace, ProfileFace
# To operate with numbers efficiently
# Loads tree and array
t = ClusterTree(tree_file, heatmap_file)
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(matrix_max,
matrix_min,
matrix_avg,
1000,
14,
"heatmap",
colorscheme=2)
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
t.show(tree_style=ts)
def layout(node):
# print node.rank
# print node.sci_name
if getattr(node, "rank", None):
if (node.rank in ['order', 'class', 'phylum', 'kingdom']):
rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
node.add_face(rank_face, column=0, position="branch-top")
if node.is_leaf():
sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
node.add_face(sciname_face, column=0, position="branch-right")
if node.is_leaf() and not node.name == 'annotation':
#here we are adding faces and we need to play with seqmotif face
seq = str(seqreclist[taxids.index(int(node.name))].seq)
motifs = [] #[[0,len(seq), "seq", 10, 10, None, None, None]]
for f in seqreclist[taxids.index(int(node.name))].features:
if f.type == 'domain':
motifs.append([
f.location.start, f.location.end, "[]", None, 10,
"blue",
get_color(f.qualifiers['name']),
"arial|8|black|%s" % f.qualifiers['name']
])
if f.type == 'motif':
#It turns out that we need to solve overlap problem here, here it is solved only in case of one overlap
s = f.location.start
e = f.location.end
flag = True
overlappedm = []
for m in motifs:
if m[2] == 'seq' and m[0] < e and m[
1] > s: #we have an overlap, four cases, preceding motife always is on top
flag = False
overlappedm.append(m)
if not flag: #we have to solve multiple overlap problem
#let's do it by scanning
sflag = False
eflag = False
for x in range(s, e + 1):
if not sflag: #check if we can start
overlap = False
for m in overlappedm:
if x >= m[0] and x < m[1]:
overlap = True
if not overlap:
ts = x
sflag = True
#check if is time to end
if sflag and not eflag:
overlap = False
for m in overlappedm:
if x == m[0]:
overlap = True
if overlap or x == e:
te = x
eflag = True
if sflag and eflag:
motifs.append([
ts, te, "seq", 10, 10, "black",
get_color(f.qualifiers['name']), None
])
sflag = False
eflag = False
if flag:
motifs.append([
f.location.start, f.location.end, "seq", 10, 10,
"black",
get_color(f.qualifiers['name']), None
])
seqFace = SeqMotifFace(seq,
motifs,
scale_factor=1,
seq_format="[]")
seqFace.overlaping_motif_opacity = 1.0
# seqFace.fg=aafgcolors
# seqFace.bg=aabgcolors_gray
add_face_to_node(seqFace, node, 0, position="aligned")
# gi=taxid2gi[int(node.name)]
add_face_to_node(
TextFace(' ' + seqreclist[taxids.index(int(node.name))].id +
' '),
node,
column=1,
position="aligned")
# add_face_to_node(TextFace(' '+str(int(node.name))+' '),node,column=2, position = "aligned")
# add_face_to_node(TextFace(' '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")
#We currently disable annotation
if node.is_leaf() and node.name == 'annotation':
if (annotation):
s = annotation
# get_hist_ss_in_aln_as_string(msa_tr)
else:
s = ' ' * max(map(lambda x: len(x.seq), seqreclist))
def my_layout(node):
# Add name label to all nodes
faces.add_face_to_node(AttrFace("name"),
node,
column=0,
position="branch-right")
