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()
if 0:
# First prepare the tree
t = func.readAndPop("29dpann_catgtr_pretty.tre")
n = t.addNodeBetweenNodes(25,26)
t.reRoot(n)
t.rotateAround(t.root)
t.writePhylip('rearrangedTree.phy')
if 1:
from Gram import TreeGram
t = func.readAndPop('rearrangedTree.phy')
# tg = TreeGram(t, yScale=0.4, widthToHeight=1.2, doNodeNums=(var.argvAfterDoubleDash[2] == "True"))
tg = TreeGram(t, yScale=0.45, doNodeNums=False)
tg.latexUsePackages.append('xcolor')
tg.latexOtherPreambleCommands.append(r"\definecolor{bact2}{HTML}{A0522D}") # Sienna
tg.latexOtherPreambleCommands.append(r"\definecolor{eury2}{HTML}{0000FF}")
tg.latexOtherPreambleCommands.append(r"\definecolor{euka2}{HTML}{31B34A}")
tg.latexOtherPreambleCommands.append(r"\definecolor{cren2}{HTML}{703E98}")
tg.latexOtherPreambleCommands.append(r"\definecolor{thau2}{HTML}{FF0000}") # Red
tg.latexOtherPreambleCommands.append(r"\definecolor{aiga2}{HTML}{FF8C00}") # Dark Orange
tg.latexOtherPreambleCommands.append(r"\definecolor{kora2}{HTML}{D11C7E}")
tg.latexOtherPreambleCommands.append(r"\definecolor{ther2}{HTML}{008080}") # Teal
tg.latexOtherPreambleCommands.append(r"\definecolor{dpan2}{HTML}{FF1493}") # Tealish
tg.latexOtherPreambleCommands.append(r"\colorlet{bact3}{bact2!20!white}")
tg.latexOtherPreambleCommands.append(r"\colorlet{eury3}{eury2!15!white}")
tg.latexOtherPreambleCommands.append(r"\colorlet{euka3}{euka2!30!white}")
tg.latexOtherPreambleCommands.append(r"\colorlet{cren3}{cren2!20!white}")
tg.latexOtherPreambleCommands.append(r"\colorlet{thau3}{thau2!30!white}")
#transfer node labels to branches
for n in t.iterInternalsNoRoot():
if n.name:
n.br.uName = n.name
n.name = None
#add new node and root on this node to create the proper effect
n = t.addNodeBetweenNodes(int(var.argvAfterDoubleDash[3]),
int(var.argvAfterDoubleDash[4]))
t.reRoot(n)
if var.argvAfterDoubleDash[5] == "y":
t.rotateAround(t.root)
#t.reRoot(int(var.argvAfterDoubleDash[2]))
tg = TreeGram(t,
yScale=0.4,
widthToHeight=1.2,
doNodeNums=(var.argvAfterDoubleDash[2] == "True"))
#tg = TreeGramRadial(t,maxLinesDim=10.,equalDaylight=False)
tg.latexUsePackages.append('pifont')
tg.latexUsePackages.append('xcolor')
tg.latexOtherPreambleCommands.append(
r"\definecolor{bact2}{HTML}{A0522D}") # Sienna
tg.latexOtherPreambleCommands.append(r"\definecolor{eury2}{HTML}{0000FF}")
tg.latexOtherPreambleCommands.append(r"\definecolor{euka2}{HTML}{31B34A}")
tg.latexOtherPreambleCommands.append(r"\definecolor{cren2}{HTML}{703E98}")
tg.latexOtherPreambleCommands.append(
r"\definecolor{thau2}{HTML}{FF0000}") # Red
tg.latexOtherPreambleCommands.append(
r"\definecolor{aiga2}{HTML}{FF8C00}") # Dark Orange
tg.latexOtherPreambleCommands.append(r"\definecolor{kora2}{HTML}{D11C7E}")
tg.latexOtherPreambleCommands.append(
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()
# n.name = ' '
#transfer node labels to branches
for n in t.iterInternalsNoRoot():
if n.name:
n.br.uName = n.name
n.name = None
#add new node and root on this node to create the proper effect
n = t.addNodeBetweenNodes(int(var.argvAfterDoubleDash[3]),int(var.argvAfterDoubleDash[4]))
t.reRoot(n)
if var.argvAfterDoubleDash[5] == "y":
t.rotateAround(t.root)
#t.reRoot(int(var.argvAfterDoubleDash[2]))
tg = TreeGram(t, yScale=0.4, widthToHeight=1.2, doNodeNums=(var.argvAfterDoubleDash[2] == "True"))
#tg = TreeGramRadial(t,maxLinesDim=10.,equalDaylight=False)
tg.latexUsePackages.append('pifont')
tg.latexUsePackages.append('xcolor')
tg.latexOtherPreambleCommands.append(r"\definecolor{bact2}{HTML}{A0522D}") # Sienna
tg.latexOtherPreambleCommands.append(r"\definecolor{eury2}{HTML}{0000FF}")
tg.latexOtherPreambleCommands.append(r"\definecolor{euka2}{HTML}{31B34A}")
tg.latexOtherPreambleCommands.append(r"\definecolor{cren2}{HTML}{703E98}")
tg.latexOtherPreambleCommands.append(r"\definecolor{thau2}{HTML}{FF0000}") # Red
tg.latexOtherPreambleCommands.append(r"\definecolor{aiga2}{HTML}{FF8C00}") # Dark Orange
tg.latexOtherPreambleCommands.append(r"\definecolor{kora2}{HTML}{D11C7E}")
tg.latexOtherPreambleCommands.append(r"\definecolor{ther2}{HTML}{008080}") # Teal
tg.latexOtherPreambleCommands.append(r"\definecolor{dpan2}{HTML}{FF1493}") # Tealish
tg.latexOtherPreambleCommands.append(r"\colorlet{bact3}{bact2!20!white}")