from gram import TreeGram
read("((A, B), (C, D), (E, (F, G)));")
t = var.trees[0]
tg = TreeGram(t, showNodeNums=False)
tg.font = 'palatino'
tg.baseName = 'bracket2'
t.draw()
longText1 = """A long note \
about this grouping of taxa, \
composed of A and B"""
b = tg.setBracket(2, 3, text=longText1, leftNode=None)
b.label.style = None
b.label.textSize = 'scriptsize'
b.label.anchor = 'west'
b.label.textWidth = 3.0
b.label.innerSep = 0.2
b = tg.setBracket(6, 10, text='Rotated label', leftNode=None, rotated=True)
b.label.textSize = 'large'
tg.bracketsLineUp = False
#tg.showTextAnchor = True
tg.png()
tg.svg()
#'node right'
#'node upper right'
#'node lower right'
#'node upper left'
#'node lower left'
my_gX = 4.0
from gram import TreeGram
myScale = 3.5
read('(((A, B)xy, (C, (D, E, F)wxyz, G))wxyz, (H, (I, J)xy)wxyz);')
t = var.trees[0]
tA = t.dupe()
tg = TreeGram(tA)
tg.baseName = 'smartNodeLabels'
tg.doSmartLabels = False # default True
tg.scale = myScale
#tg.png()
#tg.svg()
tB = t.dupe()
tgB = TreeGram(tB)
tgB.baseName = 'smart_semi'
tgB.doSmartLabels = 'semi' # default True
tgB.scale = myScale
#tgB.png()
#tgB.svg()
tg.grams.append(tgB)
tgB.gX = my_gX
from gram import TreeGram
read('(A, (B, (C, (D, (E, F))85)));')
t = var.trees[0]
tg = TreeGram(t)
tg.font = 'helvetica'
tg.baseName = 'simplified'
tg.leafLabelSize = 'tiny'
tg.render()
tg.styleDict['bracket label'].textSize = 'Large'
for n in t.iterLeavesNoRoot():
n.label.rawText = ' '
t.node(5).label.rawText = 'Euryarchaeota'
t.node(7).label.rawText = 'Crenarchaeota / eocytes'
t.node(6).label.anchor = 'north east'
g = tg.setBracket(1, 3, text='Bacteria', leftNode=0)
g.fill = 'blue!15'
g = tg.setBracket(5, 7, text='Archaea', leftNode=4)
g.fill = 'orange!20'
g = tg.setBracket(9, 10, text='Eukaryotes', leftNode=8)
g.fill = 'green!30'
tg.wrapLeafLabelsAt = 1.3 # svg can't do this
tg.pdf()
tg.wrapLeafLabelsAt = None
tg.svg()
from gram import TreeGram
read("((A,B)Wxy,(C,(D,E, F)Xyz)Vwxy);")
t = var.trees[0]
tg = TreeGram(t.dupe(),showNodeNums=True)
tg.baseName = 'stylesForInternalNodes'
tgB = TreeGram(t.dupe())
tgB.tree.node(1).label.myStyle = 'node lower left'
tgB.tree.node(4).label.myStyle = 'node right'
tgB.tree.node(6).label.myStyle = 'node lower right'
tgB.gX = 4.
tg.grams.append(tgB)
tg.svg()
from gram import TreeGram
read('((A, B)uvw, (C, D)xyz);')
t = var.trees[0]
tg = TreeGram(t.dupe(),showNodeNums=True)
tg.baseName = 'nodeLabels'
tgB = TreeGram(t.dupe())
tgB.tree.node(1).label.anchor = 'north east'
tgB.tree.node(4).label.anchor = 'west'
tgB.gX = 3.
tg.grams.append(tgB)
# tg.png()
tg.svg()
from gram import TreeGram,TreeGramRadial,Gram
read("((A,B)ab,C,(D,E)de)m;")
t = var.trees[0]
t.node(1).br.uName = 'X'
t.node(5).br.uName = 'Y'
tg = TreeGram(t, scale=7.)
print "a", tg.internalNodeLabelSize
tg.baseName = 'twoTreesII'
t = t.dupe()
tgB = TreeGramRadial(t, scale=8.,
slopedBrLabels=True,
rotate=90)
print "b", tg.internalNodeLabelSize
tgB.tree.root.label.yShift = 0.1
tgB.gX = 4.8
tgB.gY = -1.5
gr = Gram()
g = gr.text(r'$\Longleftrightarrow$', 0, 0) # LaTeX symbol
gr.text('equivalence', 0, 0.5)
gr.gX = 3.5
gr.gY = 1.0
tg.grams.append(tgB)
tg.grams.append(gr)
tg.png()
g.rawText = '⇔' # unicode symbol
tg.svg()
#'node right'
#'node upper right'
#'node lower right'
#'node upper left'
#'node lower left'
my_gX = 4.0
from gram import TreeGram
myScale = 3.5
read('(((A, B)xy, (C, (D, E, F)wxyz, G))wxyz, (H, (I, J)xy)wxyz);')
t = var.trees[0]
tA = t.dupe()
tg = TreeGram(tA)
tg.baseName = 'smartNodeLabels'
tg.doSmartLabels = False # default True
tg.scale = myScale
#tg.png()
#tg.svg()
tB = t.dupe()
tgB = TreeGram(tB)
tgB.baseName = 'smart_semi'
tgB.doSmartLabels = 'semi' # default True
tgB.scale = myScale
#tgB.png()
#tgB.svg()
tg.grams.append(tgB)
tgB.gX = my_gX
t.draw()
nB = t.node('B')
nB.name = """This is the very long name
of the node that used to be `B'. It needs
to have the text wrapped, but that affects
the spacing of the leaf taxa. Both
wrapping and spacing are handled by setting
\\texttt{wrapLeafLabelsAt}."""
nE = t.node('E')
thePng = "../../frownie_tongue.png"
nE.name = r"\includegraphics[scale=0.3]{%s}" % thePng
tg = TreeGram(t, showNodeNums=False)
tg.font = 'palatino'
tg.latexUsePackages.append('graphicx')
tg.wrapLeafLabelsAt = 3.5
tg.baseName = 'fatTaxa'
#tg.grid(0,0,5,6)
# The style gets in the way, so it is
# auto-deleted. With no style, the default
# anchor is center, so change that.
nE.label.anchor = 'west'
tg.extraYSpaceAtNode(nE, extra=1.1)
b = tg.setBracket(4, 5, text='A bracket',
leftNode=None, rotated=True)
bText = r"""Since the size of the picture is
unknown to Gram, it needed to have its
\texttt{extraYSpaceAtNode} set explicitly.
This bracket also needed to have its
\texttt{topOverRide} and
\texttt{rigthOverRide} set to some
from gram import TreeGram,TreeGramRadial
tString = "((A, (B, (C, ((D, E), F)))), G, H);"
read(tString)
t = var.trees[0]
t2 = t.dupe()
tg = TreeGram(t)
tg.baseName = 'parallelAndRadial'
#tg.grid(0,-2,10,6)
tgr = TreeGramRadial(t2, maxLinesDim=3.8)
tgr.gX = 5.0
tgr.gY = -1.0
tg.grams.append(tgr)
if 1:
g = tg.text("Parallel, using the", 0.5, -1.)
g.anchor = 'west'
g = tg.text("TreeGram class", 0.5, -1.6)
g.anchor = 'west'
g = tg.text("Radial, using the", 6.5, -1.)
g.anchor = 'west'
g = tg.text("TreeGramRadial class", 6.5, -1.6)
g.anchor = 'west'
tg.png()
tg.svg()
from gram import TreeGram
var.nexus_getAllCommandComments = True
var.nexus_readBeastTreeCommandComments = True
read('treeannotatorOut')
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'beastA'
for n in t.iterNodes():
if not n.isLeaf:
tg.setNodeConfidenceBox(n)
tg.pdf()
#tg.svg()
#the following needs modules from p4:
from p4 import *
nC.name = r'Ab{\textcolor{blue}{cde}}fgh {\textcolor{blue}{\ding{110}}}' #recognizes string to recolor parts of text and adds a square at the end
tg = TreeGram(t)
#tgr = TreeGramRadial(t) #for radial trees
n = t.node('B')
tg.setBranchULabel(n, 'uLabel') #another way using a function, when tg has been initialized
#node names - specified in newick trees? - can be accessed and modified:
#n.label.color='red!50'
#n.label.textSize='tiny' #big enough
#t.doSmartLabels=True #or 'semi'; not sure if not n.label.doSmartLabels, or even tg.doSmartLabels
#tg.fixTextOverlaps=True
tg.baseName = 'myTree'
#conf files to set some user defaults, such as font (def Helvetica)
#other useful things:
#documentFontSize
#pdfViewer
#or set these in individual gram scripts:
tg.documentFontSize = 5.5
#individually:
#tg.leafLabelSize = 'footnotesize' #LARGE compared to document fontsize
#tg.internalNodeLabelSize = 'tiny'
#tg.branchLabelSize = 'scriptsize'
tg.scale=None #use number to set 1.0 scale length in cm - then you can have the same scale for several trees
tg.setScaleBar(length=0.2, xOffset=0.0, yOffset=-0.6) #but mostly default values are okay
tg.yScale=0.7 #this is the spacing between leaves
t.draw()
nB = t.node('B')
nB.name = """This is the very long name
of the node that used to be `B'. It needs
to have the text wrapped, but that affects
the spacing of the leaf taxa. Both
wrapping and spacing are handled by setting
\\texttt{wrapLeafLabelsAt}."""
nE = t.node('E')
thePng = "../../frownie_tongue.png"
nE.name = r"\includegraphics[scale=0.3]{%s}" % thePng
tg = TreeGram(t, showNodeNums=False)
tg.font = 'palatino'
tg.latexUsePackages.append('graphicx')
tg.wrapLeafLabelsAt = 3.5
tg.baseName = 'fatTaxa'
#tg.grid(0,0,5,6)
# The style gets in the way, so it is
# auto-deleted. With no style, the default
# anchor is center, so change that.
nE.label.anchor = 'west'
tg.extraYSpaceAtNode(nE, extra=1.1)
b = tg.setBracket(4, 5, text='A bracket', leftNode=None, rotated=True)
bText = r"""Since the size of the picture is
unknown to Gram, it needed to have its
\texttt{extraYSpaceAtNode} set explicitly.
This bracket also needed to have its
\texttt{topOverRide} and
\texttt{rigthOverRide} set to some
appropriate values in order to
from gram import TreeGram
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
tg = TreeGram(t)
tg.font = 'palatino'
tg.documentFontSize = 10
tg.baseName = 'minimal_palatino'
tg.png()
tg.svg()
var.nexus_getAllCommandComments = True
var.nexus_readBeastTreeCommandComments = True
read('treeannotatorOut')
t = var.trees[0]
# The two cBoxes on the left are too big, and dominate the figure.
# Make them text, as a node labels, instead.
n = t.root
n.name = "(%.1f, %.1f)" % (n.height_95_HPD[1], n.height_95_HPD[0])
n = t.node(1)
n.name = "(%.1f, %.1f)" % (n.height_95_HPD[1], n.height_95_HPD[0])
tg = TreeGram(t)
tg.font = 'palatino'
tg.documentFontSize = 10
tg.baseName = 'beastB'
for nNum in [3, 4, 6, 9]:
n = t.node(nNum)
tg.setNodeConfidenceBox(n)
# Define a style
from gram import GramText
tg.render()
tb = GramText('myStyle')
tb.textWidth = 1.
tb.textSize = 'scriptsize'
tb.anchor = 'west'
tb.name = 'wrappedNode'
tg.styleDict['wrappedNode'] = tb
for nNum in [0, 1]:
from gram import TreeGram
read("((A,B)Wxy,(C,(D,E, F)Xyz)Vwxy);")
t = var.trees[0]
tg = TreeGram(t.dupe(), showNodeNums=True)
tg.baseName = 'stylesForInternalNodes'
tgB = TreeGram(t.dupe())
tgB.tree.node(1).label.myStyle = 'node lower left'
tgB.tree.node(4).label.myStyle = 'node right'
tgB.tree.node(6).label.myStyle = 'node lower right'
tgB.gX = 4.
tg.grams.append(tgB)
tg.svg()
from p4 import *
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
n = t.node('A')
n.name = r'Ab{\textcolor{blue}{cde}}fgh {\textcolor{blue}{\ding{110}}}'
#n.name = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ⬛</tspan>'
#n.name = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ￭</tspan>'
t.draw()
from gram import TreeGram
tg = TreeGram(t, scale=None, showNodeNums=False, widthToHeight=0.67)
tg.latexUsePackages.append('pifont')
tg.baseName = "multiBrackets"
#tg.showTextBB=True
#tg.showTextAnchor=True
#tg.pdflatexOutputGoesToDevNull=False
#tg.grid(0,0,4,4)
g = tg.setBracket(t.node('D').nodeNum,7, text="Bracket DE", rotated=True)
g = tg.setBracket(t.node('B').nodeNum,6, text="Bracket BCD", rotated=True)
g.rightExtra = 0.7
g = tg.setBracket(2,4, text="Bracket", rotated=False)
tg.bracketsLineUp = False
#tg.render()
#tg.styleDict['bracket label'].textSize = 'tiny'
tg.pdf()
n.label.rawText = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ▇</tspan>'
tg.svg()
from gram import TreeGram
read("((A, B), (C, D), (E, (F, G)));")
t = var.trees[0]
tg = TreeGram(t, showNodeNums=True)
tg.baseName = 'bracket1'
t.draw()
tg.setBracket(2, 3, text='these brackets line',
leftNode=1)
tg.setBracket(6, 10, text='up with each other',
leftNode=None, rotated=True)
tg.pdf()
tg.svg()
from gram import TreeGram
read('easyTreeA.nex')
read('easyTreeB.nex')
tA = var.trees[0]
# make a duplicate tree, as tA is used again below
tg = TreeGram(tA.dupe())
tg.baseName = 'combineSplitSupports'
tg.tree.node(8).label.myStyle = 'node upper right'
tg.tree.node(10).label.myStyle = 'node right'
tB = var.trees[1]
tgB = TreeGram(tB)
tgB.gY = -7.5
tg.grams.append(tgB)
tA.makeSplitKeys()
tB.makeSplitKeys()
nodeForSKDict = {}
for n in tB.iterInternalsNoRoot():
nodeForSKDict[n.br.splitKey] = n
for n in tA.iterInternalsNoRoot():
theNode = nodeForSKDict.get(n.br.splitKey)
if theNode:
n.name += '/%s' % theNode.name
tgX = TreeGram(tA, showNodeNums=False)
tgX.tree.node(8).label.myStyle = 'node upper right'
tgX.tree.node(10).label.myStyle = 'node right'
tgX.gY = -15.
tg.grams.append(tgX)
from gram import TreeGram
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'minimal'
tg.pdf()
from gram import TreeGram
read('tinyTree.nex')
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'tinyIII'
# styleDict is empty until you render().
tg.render()
# Grab the leaf style ...
st = tg.styleDict['leaf']
# ... and change it
st.textShape = 'itshape'
#tg.pdf()
tg.svg()
from gram import TreeGram
read("(((A, B), (C, D)));")
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'scaleBar'
tg.grid(-1, -1, 3, 3)
tg.setScaleBar(length=0.1, yOffset=-0.0)
tg.pdf()
tg.svg()
from gram import TreeGram
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
tg = TreeGram(t)
tg.font = 'palatino'
tg.documentFontSize = 10
tg.baseName = 'minimal_palatino'
tg.png()
tg.svg()
from p4 import *
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
n = t.node('A')
n.name = r'Ab{\textcolor{blue}{cde}}fgh {\textcolor{blue}{\ding{110}}}'
#n.name = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ⬛</tspan>'
#n.name = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ￭</tspan>'
t.draw()
from gram import TreeGram
tg = TreeGram(t, scale=None, showNodeNums=False, widthToHeight=0.67)
tg.latexUsePackages.append('pifont')
tg.baseName = "multiBrackets"
#tg.showTextBB=True
#tg.showTextAnchor=True
#tg.pdflatexOutputGoesToDevNull=False
#tg.grid(0,0,4,4)
g = tg.setBracket(t.node('D').nodeNum, 7, text="Bracket DE", rotated=True)
g = tg.setBracket(t.node('B').nodeNum, 6, text="Bracket BCD", rotated=True)
g.rightExtra = 0.7
g = tg.setBracket(2, 4, text="Bracket", rotated=False)
tg.bracketsLineUp = False
#tg.render()
#tg.styleDict['bracket label'].textSize = 'tiny'
tg.png()
n.label.rawText = r'Ab<tspan fill="blue">cde</tspan>fgh <tspan fill="blue"> ⬛</tspan>'
tg.svg()
from gram import TreeGram
read('tinyTree.nex')
t = var.trees[0]
tg = TreeGram(t, showNodeNums=True)
tg.baseName = 'tinyIV'
tg.font = 'helvetica'
if 1:
# Make a new style, and put it in the
# styleDict, with a name.
from gram import GramText
g = GramText("Xyx")
g.textShape = 'itshape'
g.textSize = 'small'
g.color = 'white'
g.draw = 'black'
g.lineThickness = 'very thick'
g.fill = 'blue!60'
g.name = 'myleaf'
g.anchor = 'west'
tg.styleDict[g.name] = g
# Apply the style to some of the leaves.
for nNum in [1, 4, 5, 7]: # and one internal
n = t.node(nNum)
n.label.myStyle = 'myleaf'
tg.png()
tg.svg()
from gram import TreeGram
tString = "(('TreeGram needs to', 'know how big this':0.05, 'text is':0.5), (Boojum, Snark):0.03);"
t = func.readAndPop(tString)
t.draw()
tg = TreeGram(t)
tg.font = 'helvetica'
# for nNum in [2,3,4]:
# n = t.node(nNum)
# n.label.draw = True
for nNum in [6,7]:
n = t.node(nNum)
n.label.textShape = 'itshape'
brText = "in order to place this bracket"
tg.setBracket(2,4, text=brText)
tg.baseName = 'textHowBig'
# tg.grid(0,0,5,4)
tg.pdf()
tg.svg()
from gram import TreeGram
read("(((A, B, (C, D)'a node label'):0.01, E, F)'another node label', G);")
t = var.trees[0]
tg = TreeGram(t.dupe())
tg.baseName = 'overlapping'
tgB = TreeGram(t.dupe())
tgB.fixTextOverlaps()
tgB.gX = 6
tg.grams.append(tgB)
#tg.png()
tg.svgPxForCm = 50.
tg.svg()
from gram import TreeGram
tString = "(('TreeGram needs to', 'know how big this':0.05, 'text is':0.5), (Boojum, Snark):0.03);"
t = func.readAndPop(tString)
t.draw()
tg = TreeGram(t)
# for nNum in [2,3,4]:
# n = t.node(nNum)
# n.label.draw = True
for nNum in [6, 7]:
n = t.node(nNum)
n.label.textShape = 'itshape'
brText = "in order to place this bracket"
tg.setBracket(2, 4, text=brText)
tg.baseName = 'textHowBig'
# tg.grid(0,0,5,4)
tg.pdf()
tg.svg()
from gram import TreeGram
read('tinyTree.nex')
t = var.trees[0]
tg = TreeGram(t,showNodeNums=True)
tg.baseName = 'tinyIV'
tg.font = 'helvetica'
if 1:
# Make a new style, and put it in the
# styleDict, with a name.
from gram import GramText
g = GramText("Xyx")
g.textShape = 'itshape'
g.textSize = 'small'
g.color = 'white'
g.draw = 'black'
g.lineThickness = 'very thick'
g.fill = 'blue!60'
g.name = 'myleaf'
g.anchor = 'west'
tg.styleDict[g.name] = g
# Apply the style to some of the leaves.
for nNum in [1,4,5,7]: # and one internal
n = t.node(nNum)
n.label.myStyle = 'myleaf'
tg.png()
tg.svg()
from gram import TreeGram
read('easyTreeA.nex')
read('easyTreeB.nex')
tA = var.trees[0]
# make a duplicate tree, as tA is used again below
tg = TreeGram(tA.dupe())
tg.baseName = 'combineSplitSupports'
tg.tree.node(8).label.myStyle = 'node upper right'
tg.tree.node(10).label.myStyle = 'node right'
tB = var.trees[1]
tgB = TreeGram(tB)
tgB.gY = -7.5
tg.grams.append(tgB)
tA.makeSplitKeys()
tB.makeSplitKeys()
nodeForSKDict = {}
for n in tB.iterInternalsNoRoot():
nodeForSKDict[n.br.splitKey] = n
for n in tA.iterInternalsNoRoot():
theNode = nodeForSKDict.get(n.br.splitKey)
if theNode:
n.name += '/%s' % theNode.name
tgX = TreeGram(tA, showNodeNums=False)
tgX.tree.node(8).label.myStyle = 'node upper right'
tgX.tree.node(10).label.myStyle = 'node right'
tgX.gY = -15.
tg.grams.append(tgX)
from gram import TreeGram
read("(((A, B, (C, D)'a node label'):0.01, E, F)'another node label', G);")
t = var.trees[0]
tg = TreeGram(t.dupe())
tg.baseName = 'overlapping'
tgB = TreeGram(t.dupe())
tgB.fixTextOverlaps()
tgB.gX = 6
tg.grams.append(tgB)
#tg.png()
tg.svgPxForCm = 50.
tg.svg()
from gram import TreeGram
read('((A, B), (C, (D, E)));')
t = var.trees[0]
t.draw()
nB = t.node('B')
nB.name = """synonym 1, another synonym,
and a third synonym."""
nE = t.node('D')
nE.name = """synonym 1, synonym 2,
yet another synonym, and synonym 4"""
tg = TreeGram(t, showNodeNums=False)
tg.wrapLeafLabelsAt = 'comma'
tg.baseName = 'wrapLeafLabelsAtComma'
tg.png()
# tg.svg() no workee
from gram import TreeGram
read("((A,B)89,C,(D,E)96);")
read("((H, I)73, (J, K)98, L);")
t = var.trees[0]
tg = TreeGram(t)
tg.font = 'palatino'
tg.documentFontSize = 10
tg.baseName = 'twoTrees'
t = var.trees[1]
tgB = TreeGram(t)
tgB.baseName = 'doesntMatter'
tgB.gX = 4.
tg.grams.append(tgB)
#tg.pdf()
tg.svg()
from gram import TreeGram
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'minimal'
tg.png()
from gram import TreeGram
read("((A,B)89,C,(D,E)95);")
t = var.trees[0]
tg = TreeGram(t)
tg.font = 'cm'
tg.baseName = 'minimal_cm'
tg.png()
from gram import TreeGram
read("tinyTree.nex")
t = var.trees[0]
tg = TreeGram(t)
tg.baseName = 'brokenBranches'
tg.setBrokenBranch(1)
tg.setBrokenBranch(7)
tg.png()
tg.svg()