def layout(node):
if node.is_leaf():
N = AttrFace("name", fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature 1/gini index
circle_face = CircleFace(radius=node.weight,
color="RoyalBlue",
style="sphere")
circle_face.hz_align = 2
circle_face.opacity = 0.3
text_face = TextFace(text=node.name)
faces.add_face_to_node(circle_face, node, 0, position="float")
faces.add_face_to_node(text_face, node, 0, position="float")
def my_layout(node):
circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
node.name]
text_color = 'black'
if isinstance(circle_color, str):
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': str(node.frequency),
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)
else:
P = PieChartFace(
[100 * x / node.frequency for x in circle_color.values()],
2 * 10 * scipy.sqrt(node.frequency),
2 * 10 * scipy.sqrt(node.frequency),
colors=[(color if color != 'None' else 'lightgray')
for color in list(circle_color.keys())],
line_color=None)
T = TextFace(' '.join(
[str(x) for x in list(circle_color.values())]),
tight_text=True)
T.hz_align = 1
T.rotation = -90
faces.add_face_to_node(P, node, 0, position='branch-right')
faces.add_face_to_node(T, node, 1, position='branch-right')
if idlabel:
T = TextFace(node.name, tight_text=True, fsize=6)
T.rotation = -90
T.hz_align = 1
faces.add_face_to_node(
T,
node,
1 if isinstance(circle_color, str) else 2,
position='branch-right')
def generateFigure(PF, sample, rank, input_file, output_base_name, file_type, plot_l1, scaling, output_dpi):
# Make the ETE3 tree
try:
tree = ncbi.get_topology(PF.get_all_tax_ids(sample), rank_limit=rank)
except:
logging.getLogger('Tampa').critical("Input format not compatible.")
exit(1)
ts = TreeStyle()
ts.layout_fn = PF.layout
ts.mode = "c"
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
ts.min_leaf_separation = 10
ts.arc_span = 360
#ts.legend.add_face(CircleFace(100, "#1b9e77", label="Predicted"), column=0)
#ts.legend.add_face(CircleFace(100, '#d95f02', label="True"), column=1)
# add white space to move the legend closer
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=2)
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=1)
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=0)
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=2)
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=1)
ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=0)
# add the legend
legend_fs = 50
C1 = CircleFace(100, "#1b9e77")
C1.hz_align = True
ts.legend.add_face(C1, column=0)
T1 = TextFace("Predicted", fsize=legend_fs)
T1.hz_align = True
ts.legend.add_face(T1, column=0)
if len(PF.ground_truth_dict) > 0:
C2 = CircleFace(100, "#d95f02")
C2.hz_align = True
ts.legend.add_face(C2, column=1)
T2 = TextFace("True", fsize=legend_fs)
T2.hz_align = True
ts.legend.add_face(T2, column=1)
T3 = TextFace(f"Tool: {os.path.basename(input_file).split('.')[0]}", fsize=legend_fs)
T3.hz_align = True
ts.legend.add_face(T3, column=0)
ts.allow_face_overlap = False # this lets me mess a bit with font size and face size without the interaction of the two
ts.min_leaf_separation = 10
tree_output_file = f"{output_base_name}_tree_{rank}_{sample}.{file_type}"
tree.render(tree_output_file, h=5.2, w=5, tree_style=ts, units="in", dpi=output_dpi)
if plot_l1:
# if you asked for L1 too, then plot that
true_abundance_at_rank = []
predicted_abundance_at_rank = []
for node in tree.get_leaves():
if node.rank == rank:
tax_id = str(node.taxid)
if tax_id in PF.ground_truth_tax_id_to_percentage:
true_abundance_at_rank.append(PF.ground_truth_tax_id_to_percentage[str(node.taxid)] / 100.)
else:
true_abundance_at_rank.append(0)
if tax_id in PF.profile_tax_id_to_percentage:
predicted_abundance_at_rank.append(PF.profile_tax_id_to_percentage[str(node.taxid)] / 100.)
else:
predicted_abundance_at_rank.append(0)
data = np.zeros((len(true_abundance_at_rank), 2))
data[:, 0] = np.array(true_abundance_at_rank)
data[:, 1] = np.array(predicted_abundance_at_rank)
df = pd.DataFrame(data, columns=['True', 'Predicted'])
# g = seaborn.FacetGrid(df, height=6)
ax = seaborn.scatterplot(x='True', y='Predicted', data=df, color='b', s=55)
eps = 1
ax.set_aspect('equal')
max_val = np.max(data) + eps
ax.set_xlim(-.5, max_val)
ax.set_ylim(-.5, max_val)
ax.set_xbound(-.5, max_val)
ax.set_ybound(-.5, max_val)
#plt.figure(figsize=(6,6))
plt.plot(np.linspace(0, max_val, 100), np.linspace(0, max_val, 100), color='k')
for (x, y) in zip(true_abundance_at_rank, predicted_abundance_at_rank):
if x > y:
ax.vlines(x, y, x, colors='r')
if y > x:
ax.vlines(x, x, y, colors='r')
plt.title(f"Tool: {os.path.basename(input_file).split('.')[0]}")
plt.tight_layout()
l1_out_file = f"{output_base_name}_L1_{rank}.{file_type}"
plt.savefig(l1_out_file, dpi=output_dpi)
def my_layout(node):
circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
node.name]
text_color = 'black'
if isinstance(circle_color, str):
if isolabel and hasattr(node, 'isotype'):
nl = ''.join(
sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
key=lambda x: ISO_TYPE_charORDER[x]))
else:
nl = str(node.frequency)
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': nl,
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)
else:
P = PieChartFace(
[100 * x / node.frequency for x in circle_color.values()],
2 * 10 * scipy.sqrt(node.frequency),
2 * 10 * scipy.sqrt(node.frequency),
colors=[(color if color != 'None' else 'lightgray')
for color in list(circle_color.keys())],
line_color=None)
T = TextFace(' '.join(
[str(x) for x in list(circle_color.values())]),
tight_text=True)
T.hz_align = 1
T.rotation = -90
faces.add_face_to_node(P, node, 0, position='branch-right')
faces.add_face_to_node(T, node, 1, position='branch-right')
if idlabel:
T = TextFace(node.name, tight_text=True, fsize=6)
T.rotation = -90
T.hz_align = 1
faces.add_face_to_node(
T,
node,
1 if isinstance(circle_color, str) else 2,
position='branch-right')
elif isolabel and hasattr(node, 'isotype') and False:
iso_name = ''.join(
sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
key=lambda x: ISO_TYPE_charORDER[x]))
#T = TextFace(iso_name, tight_text=True, fsize=6)
#T.rotation = -90
#T.hz_align = 1
#faces.add_face_to_node(T, node, 1 if isinstance(circle_color, str) else 2, position='branch-right')
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': iso_name,
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)