def mylayout(node):
# Internal Node formatting
nstyle = NodeStyle()
nstyle["size"] = 0
nstyle["vt_line_width"] = 2
nstyle["hz_line_width"] = 2
if node.is_leaf():
circle_face = CircleFace(10, color_dict[node.name], style='circle')
faces.add_face_to_node(circle_face,
node,
position="branch-right",
column=0)
text_face = TextFace(meta_dict[node.name][0])
text_face.fgcolor = color_dict[node.name]
faces.add_face_to_node(text_face,
node,
position="branch-right",
column=1)
node.set_style(nstyle)
elif node.is_root():
node.dist = 0
node.set_style(nstyle)
else:
node.set_style(nstyle)
def plot_tree_barplot(tree_file,
taxon2value_list_barplot,
header_list,
taxon2set2value_heatmap=False,
header_list2=False,
column_scale=True,
general_max=False,
barplot2percentage=False,
taxon2mlst=False):
'''
display one or more barplot
:param tree_file:
:param taxon2value_list:
:param exclude_outgroup:
:param bw_scale:
:param barplot2percentage: list of bool to indicates if the number are percentages and the range should be set to 0-100
:return:
'''
import matplotlib.cm as cm
from matplotlib.colors import rgb2hex
import matplotlib as mpl
if taxon2mlst:
mlst_list = list(set(taxon2mlst.values()))
mlst2color = dict(zip(mlst_list, get_spaced_colors(len(mlst_list))))
mlst2color['-'] = 'white'
if isinstance(tree_file, Tree):
t1 = tree_file
else:
t1 = Tree(tree_file)
# Calculate the midpoint node
R = t1.get_midpoint_outgroup()
# and set it as tree outgroup
t1.set_outgroup(R)
tss = TreeStyle()
value = 1
tss.draw_guiding_lines = True
tss.guiding_lines_color = "gray"
tss.show_leaf_name = False
if column_scale and header_list2:
import matplotlib.cm as cm
from matplotlib.colors import rgb2hex
import matplotlib as mpl
column2scale = {}
for column in header_list2:
values = taxon2set2value_heatmap[column].values()
norm = mpl.colors.Normalize(vmin=min(values), vmax=max(values))
cmap = cm.OrRd
m = cm.ScalarMappable(norm=norm, cmap=cmap)
column2scale[column] = m
cmap = cm.YlGnBu #YlOrRd#OrRd
values_lists = taxon2value_list_barplot.values()
scale_list = []
max_value_list = []
for n, header in enumerate(header_list):
#print 'scale', n, header
data = [float(i[n]) for i in values_lists]
if barplot2percentage is False:
max_value = max(data) #3424182#
min_value = min(data) #48.23
else:
if barplot2percentage[n] is True:
max_value = 100
min_value = 0
else:
max_value = max(data) #3424182#
min_value = min(data) #48.23
norm = mpl.colors.Normalize(vmin=min_value, vmax=max_value)
m1 = cm.ScalarMappable(norm=norm, cmap=cmap)
scale_list.append(m1)
if not general_max:
max_value_list.append(float(max_value))
else:
max_value_list.append(general_max)
for i, lf in enumerate(t1.iter_leaves()):
#if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
# lf.name = 'Pirellula staleyi DSM 6068'
# continue
if i == 0:
col_add = 0
if taxon2mlst:
header_list = ['MLST'] + header_list
for col, header in enumerate(header_list):
#lf.add_face(n, column, position="aligned")
n = TextFace(' ')
n.margin_top = 1
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 1
n.rotation = 90
n.inner_background.color = "white"
n.opacity = 1.
n.hz_align = 2
n.vt_align = 2
tss.aligned_header.add_face(n, col_add + 1)
n = TextFace('%s' % header)
n.margin_top = 1
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.inner_background.color = "white"
n.opacity = 1.
n.hz_align = 2
n.vt_align = 1
tss.aligned_header.add_face(n, col_add)
col_add += 2
if header_list2:
for col, header in enumerate(header_list2):
n = TextFace('%s' % header)
n.margin_top = 1
n.margin_right = 20
n.margin_left = 2
n.margin_bottom = 1
n.rotation = 270
n.hz_align = 2
n.vt_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, col + col_add)
if taxon2mlst:
try:
#if lf.name in leaf2mlst or int(lf.name) in leaf2mlst:
n = TextFace(' %s ' % taxon2mlst[int(lf.name)])
n.inner_background.color = 'white'
m = TextFace(' ')
m.inner_background.color = mlst2color[taxon2mlst[int(lf.name)]]
except:
n = TextFace(' na ')
n.inner_background.color = "grey"
m = TextFace(' ')
m.inner_background.color = "white"
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 0
n.margin_bottom = 2
m.margin_top = 2
m.margin_right = 0
m.margin_left = 2
m.margin_bottom = 2
lf.add_face(m, 0, position="aligned")
lf.add_face(n, 1, position="aligned")
col_add = 2
else:
col_add = 0
try:
val_list = taxon2value_list_barplot[lf.name]
except:
if not taxon2mlst:
val_list = ['na'] * len(header_list)
else:
val_list = ['na'] * (len(header_list) - 1)
for col, value in enumerate(val_list):
# show value itself
try:
n = TextFace(' %s ' % str(value))
except:
n = TextFace(' %s ' % str(value))
n.margin_top = 1
n.margin_right = 5
n.margin_left = 10
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col_add, position="aligned")
# show bar
try:
color = rgb2hex(scale_list[col].to_rgba(float(value)))
except:
color = 'white'
try:
percentage = (value / max_value_list[col]) * 100
#percentage = value
except:
percentage = 0
try:
maximum_bar = (
(max_value_list[col] - value) / max_value_list[col]) * 100
except:
maximum_bar = 0
#maximum_bar = 100-percentage
b = StackedBarFace([percentage, maximum_bar],
width=100,
height=10,
colors=[color, "white"])
b.rotation = 0
b.inner_border.color = "grey"
b.inner_border.width = 0
b.margin_right = 15
b.margin_left = 0
lf.add_face(b, col_add + 1, position="aligned")
col_add += 2
if taxon2set2value_heatmap:
shift = col + col_add + 1
i = 0
for col, col_name in enumerate(header_list2):
try:
value = taxon2set2value_heatmap[col_name][lf.name]
except:
try:
value = taxon2set2value_heatmap[col_name][int(lf.name)]
except:
value = 0
if int(value) > 0:
if int(value) > 9:
n = TextFace(' %i ' % int(value))
else:
n = TextFace(' %i ' % int(value))
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.fgcolor = "white"
n.inner_background.color = rgb2hex(
column2scale[col_name].to_rgba(
float(value))) #"orange"
n.opacity = 1.
lf.add_face(n, col + col_add, position="aligned")
i += 1
else:
n = TextFace(' ') #% str(value))
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col + col_add, position="aligned")
n = TextFace(lf.name, fgcolor="black", fsize=12, fstyle='italic')
lf.add_face(n, 0)
for n in t1.traverse():
nstyle = NodeStyle()
if n.support < 1:
nstyle["fgcolor"] = "black"
nstyle["size"] = 6
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
return t1, tss
time_begin = trackResult[r, 1]
time_end = trackResult[r, 2]
parent_id = trackResult[r, 3]
time_duration = np.abs(time_begin-time_end)
# for root
if parent_id == 0:
# Add name to root for the first iteration
root.add_feature("name", str(cell_id))
# change the branch length
root.add_feature("dist", time_duration)
#change node style
root.set_style(ns_root)
# set node name to face
nameFace = TextFace(root.name)
nameFace.fgcolor = "white"
nameFace.fsize = 15
# nameFace.border.width = 1
nameFace.background.color = "green"
node_cur.add_face(nameFace, column=1, position="branch-bottom")
else: # for child
#### search the parent node by parent_id
node_cur = root.search_nodes(name=str(parent_id))
# there should be only one parent node
if len(node_cur) == 1:
#### set child with its id
node_cur = node_cur[0].add_child(name=str(cell_id))
#### set duration
node_cur.add_feature("dist", time_duration)
def plot_ete_tree(tree_file,
ordered_queries,
leaf_id2protein_id2identity,
leaf_id2mlst,
leaf_id2spa,
leaf_id2meca,
show_identity_values=True,
leaf_id2description=False):
mlst_list = list(set(leaf_id2mlst.values()))
mlst2color = dict(zip(mlst_list, get_spaced_colors(len(mlst_list))))
mlst2color['-'] = 'white'
t1 = Tree(tree_file)
tss = TreeStyle()
R = t1.get_midpoint_outgroup()
t1.set_outgroup(R)
t1.ladderize()
head = True
column_add = 4
for lf in t1.iter_leaves():
lf.branch_vertical_margin = 0
# add MLST
if head:
n = TextFace(' MLST ')
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, 1)
if lf.name in leaf2mlst:
n = TextFace(' %s ' % leaf_id2mlst[lf.name])
n.inner_background.color = 'white'
m = TextFace(' ')
m.inner_background.color = mlst2color[leaf_id2mlst[lf.name]]
else:
n = TextFace(' na ')
n.inner_background.color = "grey"
m = TextFace(' ')
m.inner_background.color = "white"
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 0
n.margin_bottom = 2
m.margin_top = 2
m.margin_right = 0
m.margin_left = 20
m.margin_bottom = 2
lf.add_face(m, 0, position="aligned")
lf.add_face(n, 1, position="aligned")
# add spa typing
if head:
n = TextFace(' spa ')
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, column_add-2)
if lf.name in leaf_id2spa:
n = TextFace(' %s ' % leaf_id2spa[lf.name])
n.inner_background.color = "white"
else:
n = TextFace(' na ')
n.inner_background.color = "grey"
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
lf.add_face(n, column_add-2, position="aligned")
# add mecA typing
if head:
n = TextFace(' mecA ')
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, column_add-1)
if lf.name in leaf_id2meca:
n = TextFace(' %s ' % leaf_id2meca[lf.name])
if leaf_id2meca[lf.name] == 'Perfect':
n.inner_background.color = "red"
elif leaf_id2meca[lf.name] == 'Strict':
n.inner_background.color = "orange"
else:
n.inner_background.color = "white"
else:
n = TextFace(' na ')
n.inner_background.color = "grey"
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
lf.add_face(n, column_add-1, position="aligned")
# loop to add virulence gene hits
for column, protein_id in enumerate(ordered_queries):
# draw labels at the top of each column
if head:
if show_identity_values:
n = TextFace(' %s ' % str(protein_id))
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, column+column_add)
else:
n = TextFace(' %s ' % str(protein_id), fsize=6)
n.margin_top = 0
n.margin_right = 0
n.margin_left = 0
n.margin_bottom = 0
n.rotation = 270
n.vt_align = 2
n.hz_align = 2
n.inner_background.color = "white"
n.opacity = 1.
# lf.add_face(n, col, position="aligned")
tss.aligned_header.add_face(n, column+column_add)
# draw column content
if lf.name not in leaf_id2protein_id2identity:
n = TextFace(' %s ' % str(' na '))
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "grey"
lf.add_face(n, column+column_add, position="aligned")
else:
if protein_id in leaf_id2protein_id2identity[lf.name]:
identity_value = float(leaf_id2protein_id2identity[lf.name][protein_id])
color = rgb2hex(m_blue.to_rgba(identity_value))
if show_identity_values:
# report identity values in coloured boxes
# adapt box size depending the digit width
if str(identity_value) == '100.00' or str(identity_value) == '100.0':
identity_value = '100'
n = TextFace(" %s " % identity_value)
else:
n = TextFace("%.2f" % round(float(identity_value), 2))
# color text to white for dark cells
if float(identity_value) > 95:
n.fgcolor = "white"
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = color
lf.add_face(n, column+column_add, position="aligned")
else:
# draw coloured boxes without text
n = TextFace(' ')
n.margin_top = 0
n.margin_right = 0
n.margin_left = 0
n.margin_bottom = 0
# n.color = color
n.inner_background.color = color
lf.add_face(n, column+column_add, position="aligned")
else:
n = TextFace(' %s ' % str(' - '))
n.opacity = 1.
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white"
lf.add_face(n, column+column_add, position="aligned")
# end of first leaf: turn off header
head = False
# add boostrap supports
for n in t1.traverse():
nstyle = NodeStyle()
if n.support < 0.9:
nstyle["fgcolor"] = "blue"
nstyle["size"] = 6
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
return t1, tss
time_begin = trackResult[r, 1]
time_end = trackResult[r, 2]
parent_id = trackResult[r, 3]
time_duration = np.abs(time_begin - time_end)
# for root
if parent_id == 0:
# Add name to root for the first iteration
root.add_feature("name", str(cell_id))
# change the branch length
root.add_feature("dist", time_duration)
#change node style
root.set_style(ns_root)
# set node name to face
nameFace = TextFace(root.name)
nameFace.fgcolor = "white"
nameFace.fsize = 15
# nameFace.border.width = 1
nameFace.background.color = "green"
node_cur.add_face(nameFace, column=1, position="branch-bottom")
else: # for child
#### search the parent node by parent_id
node_cur = root.search_nodes(name=str(parent_id))
# there should be only one parent node
if len(node_cur) == 1:
#### set child with its id
node_cur = node_cur[0].add_child(name=str(cell_id))
#### set duration
node_cur.add_feature("dist", time_duration)
def plot_tree_stacked_barplot(
tree_file,
taxon2value_list_barplot=False,
header_list=False, # header stackedbarplots
taxon2set2value_heatmap=False,
taxon2label=False,
header_list2=False, # header counts columns
biodb=False,
column_scale=True,
general_max=False,
header_list3=False,
set2taxon2value_list_simple_barplot=False,
set2taxon2value_list_simple_barplot_counts=True,
rotate=False,
taxon2description=False):
'''
taxon2value_list_barplot list of lists:
[[bar1_part1, bar1_part2,...],[bar2_part1, bar2_part2]]
valeures de chaque liste transformes en pourcentages
:param tree_file:
:param taxon2value_list:
:param biodb:
:param exclude_outgroup:
:param bw_scale:
:return:
'''
if biodb:
from chlamdb.biosqldb import manipulate_biosqldb
server, db = manipulate_biosqldb.load_db(biodb)
taxon2description = manipulate_biosqldb.taxon_id2genome_description(
server, biodb, filter_names=True)
t1 = Tree(tree_file)
# Calculate the midpoint node
R = t1.get_midpoint_outgroup()
# and set it as tree outgroup
t1.set_outgroup(R)
colors2 = [
"red", "#FFFF00", "#58FA58", "#819FF7", "#F781F3", "#2E2E2E",
"#F7F8E0", 'black'
]
colors = [
"#7fc97f", "#386cb0", "#fdc086", "#ffffb3", "#fdb462", "#f0027f",
"#F7F8E0", 'black'
] # fdc086ff 386cb0ff f0027fff
tss = TreeStyle()
tss.draw_guiding_lines = True
tss.guiding_lines_color = "gray"
tss.show_leaf_name = False
if column_scale and header_list2:
import matplotlib.cm as cm
from matplotlib.colors import rgb2hex
import matplotlib as mpl
column2scale = {}
col_n = 0
for column in header_list2:
values = taxon2set2value_heatmap[column].values()
#print values
if min(values) == max(values):
min_val = 0
max_val = 1.5 * max(values)
else:
min_val = min(values)
max_val = max(values)
#print 'min-max', min_val, max_val
norm = mpl.colors.Normalize(vmin=min_val, vmax=max_val) # *1.1
if col_n < 4:
cmap = cm.OrRd #
else:
cmap = cm.YlGnBu #PuBu#OrRd
m = cm.ScalarMappable(norm=norm, cmap=cmap)
column2scale[column] = [m, float(max_val)] # *0.7
col_n += 1
for i, lf in enumerate(t1.iter_leaves()):
#if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
# lf.name = 'Pirellula staleyi DSM 6068'
# continue
if i == 0:
if taxon2label:
n = TextFace(' ')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.hz_align = 2
n.vt_align = 2
n.rotation = 270
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, 0)
col_add = 1
else:
col_add = 1
if header_list:
for col, header in enumerate(header_list):
n = TextFace('%s' % (header))
n.margin_top = 0
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.rotation = 270
n.hz_align = 2
n.vt_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, col + col_add)
col_add += col + 1
if header_list3:
#print 'header_list 3!'
col_tmp = 0
for header in header_list3:
n = TextFace('%s' % (header))
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.rotation = 270
n.hz_align = 2
n.vt_align = 2
n.inner_background.color = "white"
n.opacity = 1.
if set2taxon2value_list_simple_barplot_counts:
if col_tmp == 0:
col_tmp += 1
tss.aligned_header.add_face(n, col_tmp + 1 + col_add)
n = TextFace(' ')
tss.aligned_header.add_face(n, col_tmp + col_add)
col_tmp += 2
else:
tss.aligned_header.add_face(n, col_tmp + col_add)
col_tmp += 1
if set2taxon2value_list_simple_barplot_counts:
col_add += col_tmp
else:
col_add += col_tmp
if header_list2:
for col, header in enumerate(header_list2):
n = TextFace('%s' % (header))
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.rotation = 270
n.hz_align = 2
n.vt_align = 2
n.inner_background.color = "white"
n.opacity = 1.
tss.aligned_header.add_face(n, col + col_add)
col_add += col + 1
if taxon2label:
try:
n = TextFace('%s' % taxon2label[lf.name])
except:
try:
n = TextFace('%s' % taxon2label[int(lf.name)])
except:
n = TextFace('-')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
if rotate:
n.rotation = 270
lf.add_face(n, 1, position="aligned")
col_add = 2
else:
col_add = 2
if taxon2value_list_barplot:
try:
val_list_of_lists = taxon2value_list_barplot[lf.name]
except:
val_list_of_lists = taxon2value_list_barplot[int(lf.name)]
#col_count = 0
for col, value_list in enumerate(val_list_of_lists):
total = float(sum(value_list))
percentages = [(i / total) * 100 for i in value_list]
if col % 3 == 0:
col_list = colors2
else:
col_list = colors
b = StackedBarFace(percentages,
width=150,
height=18,
colors=col_list[0:len(percentages)])
b.rotation = 0
b.inner_border.color = "white"
b.inner_border.width = 0
b.margin_right = 5
b.margin_left = 5
if rotate:
b.rotation = 270
lf.add_face(b, col + col_add, position="aligned")
#col_count+=1
col_add += col + 1
if set2taxon2value_list_simple_barplot:
col_list = [
'#fc8d59', '#91bfdb', '#99d594', '#c51b7d', '#f1a340',
'#999999'
]
color_i = 0
col = 0
for one_set in header_list3:
if color_i > 5:
color_i = 0
color = col_list[color_i]
color_i += 1
# values for all taxons
values_lists = [
float(i) for i in
set2taxon2value_list_simple_barplot[one_set].values()
]
#print values_lists
#print one_set
value = set2taxon2value_list_simple_barplot[one_set][lf.name]
if set2taxon2value_list_simple_barplot_counts:
if isinstance(value, float):
a = TextFace(" %s " % str(round(value, 2)))
else:
a = TextFace(" %s " % str(value))
a.margin_top = 1
a.margin_right = 2
a.margin_left = 5
a.margin_bottom = 1
if rotate:
a.rotation = 270
lf.add_face(a, col + col_add, position="aligned")
#print 'value and max', value, max(values_lists)
fraction_biggest = (float(value) / max(values_lists)) * 100
fraction_rest = 100 - fraction_biggest
#print 'fractions', fraction_biggest, fraction_rest
b = StackedBarFace([fraction_biggest, fraction_rest],
width=100,
height=15,
colors=[color, 'white'])
b.rotation = 0
b.inner_border.color = "grey"
b.inner_border.width = 0
b.margin_right = 15
b.margin_left = 0
if rotate:
b.rotation = 270
if set2taxon2value_list_simple_barplot_counts:
if col == 0:
col += 1
lf.add_face(b, col + 1 + col_add, position="aligned")
col += 2
else:
lf.add_face(b, col + col_add, position="aligned")
col += 1
if set2taxon2value_list_simple_barplot_counts:
col_add += col
else:
col_add += col
if taxon2set2value_heatmap:
i = 0
#if not taxon2label:
# col_add-=1
for col2, head in enumerate(header_list2):
col_name = header_list2[i]
try:
value = taxon2set2value_heatmap[col_name][str(lf.name)]
except:
try:
value = taxon2set2value_heatmap[col_name][round(
float(lf.name), 2)]
except:
value = 0
if header_list2[i] == 'duplicates':
print('dupli', lf.name, value)
#print 'val----------------', value
if int(value) > 0:
if int(value) >= 10 and int(value) < 100:
n = TextFace('%4i' % value)
elif int(value) >= 100:
n = TextFace('%3i' % value)
else:
n = TextFace('%5i' % value)
n.margin_top = 1
n.margin_right = 2
n.margin_left = 5
n.margin_bottom = 1
n.hz_align = 1
n.vt_align = 1
if rotate:
n.rotation = 270
n.inner_background.color = rgb2hex(
column2scale[col_name][0].to_rgba(
float(value))) #"orange"
#print 'xaxaxaxaxa', value,
if float(value) > column2scale[col_name][1]:
n.fgcolor = 'white'
n.opacity = 1.
n.hz_align = 1
n.vt_align = 1
lf.add_face(n, col2 + col_add, position="aligned")
i += 1
else:
n = TextFace('')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 5
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
if rotate:
n.rotation = 270
lf.add_face(n, col2 + col_add, position="aligned")
i += 1
#lf.name = taxon2description[lf.name]
n = TextFace(taxon2description[lf.name],
fgcolor="black",
fsize=12,
fstyle='italic')
lf.add_face(n, 0)
for n in t1.traverse():
nstyle = NodeStyle()
if n.support < 1:
nstyle["fgcolor"] = "black"
nstyle["size"] = 6
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
return t1, tss
def plot_heatmap_tree_locus(biodb,
tree_file,
taxid2count,
taxid2identity=False,
taxid2locus=False,
reference_taxon=False,
n_paralogs_barplot=False):
'''
plot tree and associated heatmap with count of homolgs
optional:
- add identity of closest homolog
- add locus tag of closest homolog
'''
from chlamdb.biosqldb import manipulate_biosqldb
server, db = manipulate_biosqldb.load_db(biodb)
taxid2organism = manipulate_biosqldb.taxon_id2genome_description(
server, biodb, True)
t1 = Tree(tree_file)
ts = TreeStyle()
ts.draw_guiding_lines = True
ts.guiding_lines_color = "gray"
# Calculate the midpoint node
R = t1.get_midpoint_outgroup()
# and set it as tree outgroup
t1.set_outgroup(R)
leaf_number = 0
for lf in t1.iter_leaves():
if str(lf.name) not in taxid2count:
taxid2count[str(lf.name)] = 0
max_count = max([taxid2count[str(lf.name)] for lf in t1.iter_leaves()])
for i, lf in enumerate(t1.iter_leaves()):
# top leaf, add header
if i == 0:
n = TextFace('Number of homologs')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
n.rotation = -25
#lf.add_face(n, 7, position="aligned")
ts.aligned_header.add_face(n, 1)
if taxid2identity:
n = TextFace('Protein identity')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
n.rotation = -25
#lf.add_face(n, 7, position="aligned")
ts.aligned_header.add_face(n, 2)
if taxid2locus:
n = TextFace('Locus tag')
n.margin_top = 1
n.margin_right = 1
n.margin_left = 20
n.margin_bottom = 1
n.inner_background.color = "white"
n.opacity = 1.
n.rotation = -25
#lf.add_face(n, 7, position="aligned")
ts.aligned_header.add_face(n, 3)
leaf_number += 1
lf.branch_vertical_margin = 0
data = [taxid2count[str(lf.name)]]
# possibility to add one or more columns
for col, value in enumerate(data):
col_index = col
if value > 0:
n = TextFace(' %s ' % str(value))
n.margin_top = 2
n.margin_right = 2
if col == 0:
n.margin_left = 20
else:
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white" # #81BEF7
n.opacity = 1.
lf.add_face(n, col, position="aligned")
else:
n = TextFace(' %s ' % str(value))
n.margin_top = 2
n.margin_right = 2
if col == 0:
n.margin_left = 20
else:
n.margin_left = 2
n.margin_bottom = 2
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col, position="aligned")
# optionally indicate number of paralogs as a barplot
if n_paralogs_barplot:
col_index += 1
percent = (float(value) / max_count) * 100
n = StackedBarFace([percent, 100 - percent],
width=150,
height=18,
colors=['#6699ff', 'white'],
line_color='white')
n.rotation = 0
n.inner_border.color = "white"
n.inner_border.width = 0
n.margin_right = 15
n.margin_left = 0
lf.add_face(n, col + 1, position="aligned")
# optionally add additionnal column with identity
if taxid2identity:
import matplotlib.cm as cm
from matplotlib.colors import rgb2hex
import matplotlib as mpl
norm = mpl.colors.Normalize(vmin=0, vmax=100)
cmap = cm.OrRd
m = cm.ScalarMappable(norm=norm, cmap=cmap)
try:
if round(taxid2identity[str(lf.name)], 2) != 100:
value = "%.2f" % round(taxid2identity[str(lf.name)], 2)
else:
value = "%.1f" % round(taxid2identity[str(lf.name)], 2)
except:
value = '-'
if str(lf.name) == str(reference_taxon):
value = ' '
n = TextFace(' %s ' % value)
n.margin_top = 2
n.margin_right = 2
n.margin_left = 20
n.margin_bottom = 2
if not value.isspace() and value is not '-':
n.inner_background.color = rgb2hex(m.to_rgba(float(value)))
if float(value) > 82:
n.fgcolor = 'white'
n.opacity = 1.
if str(lf.name) == str(reference_taxon):
n.inner_background.color = '#800000'
lf.add_face(n, col_index + 1, position="aligned")
# optionaly add column with locus name
if taxid2locus:
try:
value = str(taxid2locus[str(lf.name)])
except:
value = '-'
n = TextFace(' %s ' % value)
n.margin_top = 2
n.margin_right = 2
n.margin_left = 2
n.margin_bottom = 2
if str(lf.name) != str(reference_taxon):
n.inner_background.color = "white"
else:
n.fgcolor = '#ff0000'
n.inner_background.color = "white"
n.opacity = 1.
lf.add_face(n, col_index + 2, position="aligned")
lf.name = taxid2organism[str(lf.name)]
return t1, leaf_number, ts
