def plot_tree(tree, base_name='tree', dir_name='gram'):
read(tree)
t = var.trees[-1]
for n in t.iterNodes():
if n.isLeaf:
try:
img = Image.open(get_image_path(n.name))
except IOError as e:
print n.name
raise e
w, h = img.size
width, height = None, 6.5
if w > h and (n.name in _wide_images):
width, height = 12, None
vmargin = 0
lmargin = 11
dimension_name = 'height'
dimension = height
if height is None:
dimension_name = 'width'
dimension = width
node_name = n.name
n.name = r"\hspace{{{0}mm}}\includegraphics[{1}={2}mm,resolution=150]{{{3}}}".format(
lmargin, dimension_name, dimension, get_image_path(node_name))
tg = TreeGram(t, yScale=0.8, widthToHeight=0.8)
tg.tgDefaultLineThickness = 'very thick'
tg.baseName = base_name
tg.dirName = dir_name
tg.epdf()
def plot_tree(tree, base_name = 'tree', dir_name = 'gram'):
read(tree)
t = var.trees[-1]
for n in t.iterNodes():
if n.isLeaf:
try:
img = Image.open(get_image_path(n.name))
except IOError as e:
print n.name
raise e
w, h = img.size
width, height = None, 6.5
if w > h and (n.name in _wide_images):
width, height = 12, None
vmargin = 0
lmargin = 11
dimension_name = 'height'
dimension = height
if height is None:
dimension_name = 'width'
dimension = width
node_name = n.name
n.name = r"\hspace{{{0}mm}}\includegraphics[{1}={2}mm,resolution=150]{{{3}}}".format(
lmargin,
dimension_name,
dimension,
get_image_path(node_name))
tg = TreeGram(t, yScale=0.8, widthToHeight=0.8)
tg.tgDefaultLineThickness = 'very thick'
tg.baseName = base_name
tg.dirName = dir_name
tg.epdf()
g.fill = 'bact3'
g = tg.setBracket(17,26, text = "Euryarchaeota", leftNode=16)
g.fill = 'eury3'
g = tg.setBracket(29,29, text = "Korarchaeota", leftNode=28)
g.fill = 'kora3'
tg.bracketsLineUp = False
#tg.leafLabelSize = 'normalsize'
#tg.internalNodeLabelSize = 'normalsize'
tg.branchLabelSize = tg.internalNodeLabelSize
tg.tgDefaultLineThickness = 'thick' # default 'semithick'
#tg.setScaleBar(yOffset = -1.0,length=0.2)
tg.setScaleBar(length=0.2)
tg.setBrokenBranch(72)
n = t.node(1)
tg.setBranchLabel(n, "1")
# Only one tweak needed, for node 16.
# Note that the label is adjusted, not the node.
t.node(16).label.xShift = -0.25
tg.render()
st = tg.tikzStyleDict['bracket label']
st.textShape = 'itshape'
st.textSize = 'large'
st = tg.tikzStyleDict['leaf']
st.textShape = 'itshape'
tg.epdf()
def plot_tree(tree, base_name="tree", dir_name="gram", show_events=False):
read(tree)
print var.trees
t = var.trees[-1]
for n in t.iterNodes():
if n.isLeaf:
try:
img = Image.open(get_image_path(n.name))
except IOError as e:
print n.name
raise e
w, h = img.size
width, height = None, 6.5
if w > h and (n.name in _wide_images):
width, height = 8, None
vmargin = 0
lmargin = 9
dimension_name = "height"
dimension = height
if height is None:
dimension_name = "width"
dimension = width
node_name = n.name
if node_name in _extinct_images:
lmargin += 2
n.name = r"\hspace{{{0}mm}}\includegraphics[{1}={2}mm,resolution=150]{{{3}}}".format(
lmargin, dimension_name, dimension, get_image_path(node_name)
)
tg = TreeGram(t, yScale=0.65, widthToHeight=1.3)
tg.tgDefaultLineThickness = "very thick"
tg.baseName = base_name
tg.dirName = dir_name
l1 = tg.gramLine(6.34, -0.5, 6.34, 11)
# l1.lineStyle = 'loosely dashed'
# l1.lineThickness = 'ultra thick'
l1.lineThickness = 10.0
l2 = tg.gramLine(13.4, -0.5, 13.4, 11)
# l2.lineStyle = 'loosely dashed'
# l2.lineThickness = 'ultra thick'
l2.lineThickness = 10.0
l1.colour = "black!40"
l2.colour = "black!40"
if not show_events:
# print dir(l1)
l1.colour = "black!00"
l2.colour = "black!00"
s = tg.code(
r"""\draw [draw=none] (10.97, 9.75) node[circle, minimum width=10pt, draw=none, inner sep=0pt, path picture={\draw[red] (path picture bounding box.south east) -- (path picture bounding box.north west) (path picture bounding box.south west) -- (path picture bounding box.north east);}] {};"""
)
if tree == _sec_tree:
s = tg.code(
r"""\draw [draw=none] (7.08, 10.4) node[circle, minimum width=10pt, draw=none, inner sep=0pt, path picture={\draw[red] (path picture bounding box.south east) -- (path picture bounding box.north west) (path picture bounding box.south west) -- (path picture bounding box.north east);}] {};"""
)
s = tg.code(
r"""\draw [draw=none] (13.17, 7.15) node[circle, minimum width=10pt, draw=none, inner sep=0pt, path picture={\draw[red] (path picture bounding box.south east) -- (path picture bounding box.north west) (path picture bounding box.south west) -- (path picture bounding box.north east);}] {};"""
)
else:
s = tg.code(
r"""\draw [draw=none] (6.34, 10.4) node[circle, minimum width=10pt, draw=none, inner sep=0pt, path picture={\draw[red] (path picture bounding box.south east) -- (path picture bounding box.north west) (path picture bounding box.south west) -- (path picture bounding box.north east);}] {};"""
)
s = tg.code(
r"""\draw [draw=none] (13.4, 7.15) node[circle, minimum width=10pt, draw=none, inner sep=0pt, path picture={\draw[red] (path picture bounding box.south east) -- (path picture bounding box.north west) (path picture bounding box.south west) -- (path picture bounding box.north east);}] {};"""
)
tg.epdf()