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}")

tg.latexOtherPreambleCommands.append(r"\colorlet{aiga3}{aiga2!30!white}")

tg.latexOtherPreambleCommands.append(r"\colorlet{kora3}{kora2!30!white}")

tg.latexOtherPreambleCommands.append(r"\colorlet{ther3}{ther2!30!white}")

tg.latexOtherPreambleCommands.append(r"\colorlet{dpan3}{dpan2!30!white}")

tg.font = 'helvetica'

tg.documentFontSize=11

tg.pdfViewer = 'open'

if 1:

g = tg.setBracket(31,48, text = "Eukaryotes", leftNode=30)

g.fill = 'euka3'

g = tg.setBracket(59,71, text = "Crenarchaeota", leftNode=57)

g.fill = 'cren3'

g = tg.setBracket(53,55, text = "Thaumarchaeota", leftNode=51)

g.fill = 'thau3'

g = tg.setBracket(56,56, text = "Aigarchaeota", leftNode=50)

g.fill = 'aiga3'

g = tg.setBracket(5,14, text = "DPANN", leftNode=2)

g.fill = 'dpan3'

g = tg.setBracket(74,86, text = "Bacteria", leftNode=72)

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()