def get_example_tree():
t = Tree("((a,b),c);")
right_c0_r0 = TextFace("right_col0_row0")
right_c0_r1 = TextFace("right_col0_row1")
right_c1_r0 = TextFace("right_col1_row0")
right_c1_r1 = TextFace("right_col1_row1")
right_c1_r2 = TextFace("right_col1_row2")
top_c0_r0 = TextFace("top_col0_row0")
top_c0_r1 = TextFace("top_col0_row1")
bottom_c0_r0 = TextFace("bottom_col0_row0")
bottom_c1_r0 = TextFace("bottom_col1_row0")
aligned_c0_r0 = TextFace("aligned_col0_row0")
aligned_c0_r1 = TextFace("aligned_col0_row1")
aligned_c1_r0 = TextFace("aligned_col1_row0")
aligned_c1_r1 = TextFace("aligned_col1_row1")
t.add_face(right_c0_r1, column=1, position="branch-right")
t.add_face(right_c0_r0, column=0, position="branch-right")
t.add_face(right_c1_r2, column=2, position="branch-right")
t.add_face(right_c1_r1, column=1, position="branch-right")
t.add_face(right_c1_r0, column=0, position="branch-right")
t.add_face(top_c0_r1, column=1, position="branch-top")
t.add_face(top_c0_r0, column=0, position="branch-top")
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c1_r0, column=1, position="branch-bottom")
for leaf in t.iter_leaves():
leaf.add_face(aligned_c0_r1, 0, "aligned")
leaf.add_face(aligned_c0_r0, 0, "aligned")
leaf.add_face(aligned_c1_r1, 0, "aligned")
leaf.add_face(aligned_c1_r0, 0, "aligned")
return t, TreeStyle()
def get_example_tree():
t = Tree("((a,b),c);")
right_c0_r0 = TextFace("right_col0_row0")
right_c0_r1 = TextFace("right_col0_row1")
right_c1_r0 = TextFace("right_col1_row0")
right_c1_r1 = TextFace("right_col1_row1")
right_c1_r2 = TextFace("right_col1_row2")
top_c0_r0 = TextFace("top_col0_row0")
top_c0_r1 = TextFace("top_col0_row1")
bottom_c0_r0 = TextFace("bottom_col0_row0")
bottom_c1_r0 = TextFace("bottom_col1_row0")
aligned_c0_r0 = TextFace("aligned_col0_row0")
aligned_c0_r1 = TextFace("aligned_col0_row1")
aligned_c1_r0 = TextFace("aligned_col1_row0")
aligned_c1_r1 = TextFace("aligned_col1_row1")
t.add_face(right_c0_r1, column=1, position="branch-right")
t.add_face(right_c0_r0, column=0, position="branch-right")
t.add_face(right_c1_r2, column=2, position="branch-right")
t.add_face(right_c1_r1, column=1, position="branch-right")
t.add_face(right_c1_r0, column=0, position="branch-right")
t.add_face(top_c0_r1, column=1, position="branch-top")
t.add_face(top_c0_r0, column=0, position="branch-top")
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c1_r0, column=1, position="branch-bottom")
for leaf in t.iter_leaves():
leaf.add_face(aligned_c0_r1, 0, "aligned")
leaf.add_face(aligned_c0_r0, 0, "aligned")
leaf.add_face(aligned_c1_r1, 0, "aligned")
leaf.add_face(aligned_c1_r0, 0, "aligned")
return t, TreeStyle()
def get_example_tree():
t = Tree()
t.populate(10)
# Margins, alignment, border, background and opacity can now be set for any face
rs1 = faces.TextFace("branch-right\nmargins&borders",
fsize=12,
fgcolor="#009000")
rs1.margin_top = 10
rs1.margin_bottom = 50
rs1.margin_left = 40
rs1.margin_right = 40
rs1.border.width = 1
rs1.background.color = "lightgreen"
rs1.inner_border.width = 0
rs1.inner_border.line_style = 1
rs1.inner_border.color = "red"
rs1.opacity = 0.6
rs1.hz_align = 2 # 0 left, 1 center, 2 right
rs1.vt_align = 1 # 0 left, 1 center, 2 right
br1 = faces.TextFace("branch-right1", fsize=12, fgcolor="#009000")
br2 = faces.TextFace("branch-right3", fsize=12, fgcolor="#009000")
# New face positions (branch-top and branch-bottom)
bb = faces.TextFace("branch-bottom 1", fsize=8, fgcolor="#909000")
bb2 = faces.TextFace("branch-bottom 2", fsize=8, fgcolor="#909000")
bt = faces.TextFace("branch-top 1", fsize=6, fgcolor="#099000")
# And faces can also be used as headers or foot notes of aligned
# columns
t1 = faces.TextFace("Header Face", fsize=12, fgcolor="#aa0000")
t2 = faces.TextFace("Footer Face", fsize=12, fgcolor="#0000aa")
# Attribute faces can now contain prefix and suffix fixed text
aligned = faces.AttrFace("name",
fsize=12,
fgcolor="RoyalBlue",
text_prefix="Aligned (",
text_suffix=")")
# horizontal and vertical alignment per face
aligned.hz_align = 1 # 0 left, 1 center, 2 right
aligned.vt_align = 1
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
style = NodeStyle()
style["fgcolor"] = "Gold"
style["shape"] = "square"
style["size"] = 15
style["vt_line_color"] = "#ff0000"
t.set_style(style)
# add a face to the style. This face will be render in any node
# associated to the style.
fixed = faces.TextFace("FIXED branch-right", fsize=11, fgcolor="blue")
t.add_face(fixed, column=1, position="branch-right")
# Bind the precomputed style to the root node
# ETE 2.1 has now support for general image properties
ts = TreeStyle()
# You can add faces to the tree image (without any node
# associated). They will be used as headers and foot notes of the
# aligned columns (aligned faces)
ts.aligned_header.add_face(t1, column=0)
ts.aligned_header.add_face(t1, 1)
ts.aligned_header.add_face(t1, 2)
ts.aligned_header.add_face(t1, 3)
t1.hz_align = 1 # 0 left, 1 center, 2 right
t1.border.width = 1
ts.aligned_foot.add_face(t2, column=0)
ts.aligned_foot.add_face(t2, 1)
ts.aligned_foot.add_face(t2, 2)
ts.aligned_foot.add_face(t2, 3)
t2.hz_align = 1
# Set tree image style. Note that aligned header and foot is only
# visible in "rect" mode.
ts.mode = "r"
ts.scale = 10
for node in t.traverse():
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
node.add_face(aligned, column=0, position="aligned")
node.add_face(aligned, column=1, position="aligned")
node.add_face(aligned, column=3, position="aligned")
else:
node.add_face(bt, column=0, position="branch-top")
node.add_face(bb, column=0, position="branch-bottom")
node.add_face(bb2, column=0, position="branch-bottom")
node.add_face(br1, column=0, position="branch-right")
node.add_face(rs1, column=0, position="branch-right")
node.add_face(br2, column=0, position="branch-right")
return t, ts
right_c1_r2 = TextFace("right_col1_row2")
top_c0_r0 = TextFace("top_col0_row0")
top_c0_r1 = TextFace("top_col0_row1")
bottom_c0_r0 = TextFace("bottom_col0_row0")
bottom_c1_r0 = TextFace("bottom_col1_row0")
aligned_c0_r0 = TextFace("aligned_col0_row0")
aligned_c0_r1 = TextFace("aligned_col0_row1")
aligned_c1_r0 = TextFace("aligned_col1_row0")
aligned_c1_r1 = TextFace("aligned_col1_row1")
t.add_face(right_c0_r1, column=1, position="branch-right")
t.add_face(right_c0_r0, column=0, position="branch-right")
t.add_face(right_c1_r2, column=2, position="branch-right")
t.add_face(right_c1_r1, column=1, position="branch-right")
t.add_face(right_c1_r0, column=0, position="branch-right")
t.add_face(top_c0_r1, column=1, position="branch-top")
t.add_face(top_c0_r0, column=0, position="branch-top")
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c1_r0, column=1, position="branch-bottom")
for leaf in t.iter_leaves():
leaf.add_face(aligned_c0_r1, 0, "aligned")
leaf.add_face(aligned_c0_r0, 0, "aligned")
def get_example_tree():
t = Tree()
t.populate(10)
# Margins, alignment, border, background and opacity can now be set for any face
rs1 = faces.TextFace("branch-right\nmargins&borders",
fsize=12, fgcolor="#009000")
rs1.margin_top = 10
rs1.margin_bottom = 50
rs1.margin_left = 40
rs1.margin_right = 40
rs1.border.width = 1
rs1.background.color = "lightgreen"
rs1.inner_border.width = 0
rs1.inner_border.line_style = 1
rs1.inner_border.color= "red"
rs1.opacity = 0.6
rs1.hz_align = 2 # 0 left, 1 center, 2 right
rs1.vt_align = 1 # 0 left, 1 center, 2 right
br1 = faces.TextFace("branch-right1", fsize=12, fgcolor="#009000")
br2 = faces.TextFace("branch-right3", fsize=12, fgcolor="#009000")
# New face positions (branch-top and branch-bottom)
bb = faces.TextFace("branch-bottom 1", fsize=8, fgcolor="#909000")
bb2 = faces.TextFace("branch-bottom 2", fsize=8, fgcolor="#909000")
bt = faces.TextFace("branch-top 1", fsize=6, fgcolor="#099000")
# And faces can also be used as headers or foot notes of aligned
# columns
t1 = faces.TextFace("Header Face", fsize=12, fgcolor="#aa0000")
t2 = faces.TextFace("Footer Face", fsize=12, fgcolor="#0000aa")
# Attribute faces can now contain prefix and suffix fixed text
aligned = faces.AttrFace("name", fsize=12, fgcolor="RoyalBlue",
text_prefix="Aligned (", text_suffix=")")
# horizontal and vertical alignment per face
aligned.hz_align = 1 # 0 left, 1 center, 2 right
aligned.vt_align = 1
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
style = NodeStyle()
style["fgcolor"] = "Gold"
style["shape"] = "square"
style["size"] = 15
style["vt_line_color"] = "#ff0000"
t.set_style(style)
# add a face to the style. This face will be render in any node
# associated to the style.
fixed = faces.TextFace("FIXED branch-right", fsize=11, fgcolor="blue")
t.add_face(fixed, column=1, position="branch-right")
# Bind the precomputed style to the root node
# ETE 2.1 has now support for general image properties
ts = TreeStyle()
# You can add faces to the tree image (without any node
# associated). They will be used as headers and foot notes of the
# aligned columns (aligned faces)
ts.aligned_header.add_face(t1, column = 0)
ts.aligned_header.add_face(t1, 1)
ts.aligned_header.add_face(t1, 2)
ts.aligned_header.add_face(t1, 3)
t1.hz_align = 1 # 0 left, 1 center, 2 right
t1.border.width = 1
ts.aligned_foot.add_face(t2, column = 0)
ts.aligned_foot.add_face(t2, 1)
ts.aligned_foot.add_face(t2, 2)
ts.aligned_foot.add_face(t2, 3)
t2.hz_align = 1
# Set tree image style. Note that aligned header and foot is only
# visible in "rect" mode.
ts.mode = "r"
ts.scale = 10
for node in t.traverse():
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
node.add_face(aligned, column=0, position="aligned")
node.add_face(aligned, column=1, position="aligned")
node.add_face(aligned, column=3, position="aligned")
else:
node.add_face(bt, column=0, position="branch-top")
node.add_face(bb, column=0, position="branch-bottom")
node.add_face(bb2, column=0, position="branch-bottom")
node.add_face(br1, column=0, position="branch-right")
node.add_face(rs1, column=0, position="branch-right")
node.add_face(br2, column=0, position="branch-right")
return t, ts
aligned.vt_align = 1
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
style = NodeStyle()
style["fgcolor"] = "Gold"
style["shape"] = "square"
style["size"] = 15
style["vt_line_color"] = "#ff0000"
t.set_style(style)
# add a face to the style. This face will be render in any node
# associated to the style.
fixed = faces.TextFace("FIXED branch-right", fsize=11, fgcolor="blue")
t.add_face(fixed, column=1, position="branch-right")
# Bind the precomputed style to the root node
# ETE 2.1 has now support for general image properties
I = TreeStyle()
# You can add faces to the tree image (without any node
# associated). They will be used as headers and foot notes of the
# aligned columns (aligned faces)
I.aligned_header.add_face(t1, column = 0)
I.aligned_header.add_face(t1, 1)
I.aligned_header.add_face(t1, 2)
I.aligned_header.add_face(t1, 3)
t1.hz_align = 1 # 0 left, 1 center, 2 right
t1.border.width = 1
