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Merged
merged 1 commit into from
Dec 16, 2024
Merged

:format: format with black, lint with ruff #2

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11 changes: 5 additions & 6 deletions .github/workflows/cdci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ on:
types: [published]

jobs:
# format:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - uses: psf/black@stable
format:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
# lint:
# name: Lint with ruff
# runs-on: ubuntu-latest
Expand Down Expand Up @@ -51,7 +51,6 @@ jobs:
pip install -e .
# - name: Run tests
# run: python -m pytest tests



publish:
Expand Down
215 changes: 135 additions & 80 deletions src/vuecore/Dendrogram.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,19 @@
from collections import OrderedDict
import plotly.graph_objs as go

def plot_dendrogram(Z_dendrogram, cutoff_line=True, value=15, orientation='bottom', hang=30, hide_labels=False, labels=None,
colorscale=None, hovertext=None, color_threshold=None):

def plot_dendrogram(
Z_dendrogram,
cutoff_line=True,
value=15,
orientation="bottom",
hang=30,
hide_labels=False,
labels=None,
colorscale=None,
hovertext=None,
color_threshold=None,
):
"""
Modified version of Plotly _dendrogram.py that returns a dendrogram Plotly figure object with cutoff line.

Expand Down Expand Up @@ -36,25 +47,59 @@ def plot_dendrogram(Z_dendrogram, cutoff_line=True, value=15, orientation='botto
figure = plot_dendrogram(dendro_tree, hang=0.9, cutoff_line=False)
"""

dendrogram = Dendrogram(Z_dendrogram, orientation, hang, hide_labels, labels, colorscale, hovertext=hovertext, color_threshold=color_threshold)
dendrogram = Dendrogram(
Z_dendrogram,
orientation,
hang,
hide_labels,
labels,
colorscale,
hovertext=hovertext,
color_threshold=color_threshold,
)

if cutoff_line == True:
dendrogram.layout.update({'shapes':[{'type':'line',
'xref':'paper',
'yref':'y',
'x0':0, 'y0':value,
'x1':1, 'y1':value,
'line':{'color':'red'}}]})
dendrogram.layout.update(
{
"shapes": [
{
"type": "line",
"xref": "paper",
"yref": "y",
"x0": 0,
"y0": value,
"x1": 1,
"y1": value,
"line": {"color": "red"},
}
]
}
)

figure = dict(data=dendrogram.data, layout=dendrogram.layout)
figure['layout']['template'] = 'plotly_white'
figure["layout"]["template"] = "plotly_white"

return figure


class Dendrogram(object):
"""Refer to plot_dendrogram() for docstring."""
def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False, labels=None, colorscale=None, hovertext=None,
color_threshold=None, width=np.inf, height=np.inf, xaxis='xaxis', yaxis='yaxis'):

def __init__(
self,
Z_dendrogram,
orientation="bottom",
hang=1,
hide_labels=False,
labels=None,
colorscale=None,
hovertext=None,
color_threshold=None,
width=np.inf,
height=np.inf,
xaxis="xaxis",
yaxis="yaxis",
):
self.orientation = orientation
self.labels = labels
self.xaxis = xaxis
Expand All @@ -64,20 +109,19 @@ def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False
self.sign = {self.xaxis: 1, self.yaxis: 1}
self.layout = {self.xaxis: {}, self.yaxis: {}}

if self.orientation in ['left', 'bottom']:
if self.orientation in ["left", "bottom"]:
self.sign[self.xaxis] = 1
else:
self.sign[self.xaxis] = -1

if self.orientation in ['right', 'bottom']:
if self.orientation in ["right", "bottom"]:
self.sign[self.yaxis] = 1
else:
self.sign[self.yaxis] = -1

(dd_traces, xvals, yvals,
ordered_labels, leaves) = self.get_dendrogram_traces(Z_dendrogram, hang, colorscale,
hovertext,
color_threshold)
(dd_traces, xvals, yvals, ordered_labels, leaves) = self.get_dendrogram_traces(
Z_dendrogram, hang, colorscale, hovertext, color_threshold
)

self.labels = ordered_labels
self.leaves = leaves
Expand All @@ -93,9 +137,9 @@ def __init__(self, Z_dendrogram, orientation='bottom', hang=1, hide_labels=False
if len(self.zero_vals) > len(yvals) + 1:
l_border = int(min(self.zero_vals))
r_border = int(max(self.zero_vals))
correct_leaves_pos = range(l_border,
r_border + 1,
int((r_border - l_border) / len(yvals)))
correct_leaves_pos = range(
l_border, r_border + 1, int((r_border - l_border) / len(yvals))
)
self.zero_vals = [v for v in correct_leaves_pos]

self.zero_vals.sort()
Expand All @@ -113,26 +157,29 @@ def get_color_dict(self, colorscale):

# These are the color codes returned for dendrograms
# We're replacing them with nicer colors
d = {'r': 'red',
'g': 'green',
'b': 'blue',
'c': 'cyan',
'm': 'magenta',
'y': 'yellow',
'k': 'black',
'w': 'white'}
d = {
"r": "red",
"g": "green",
"b": "blue",
"c": "cyan",
"m": "magenta",
"y": "yellow",
"k": "black",
"w": "white",
}
default_colors = OrderedDict(sorted(d.items(), key=lambda t: t[0]))

if colorscale is None:
colorscale = [
'rgb(0,116,217)', # blue
'rgb(35,205,205)', # cyan
'rgb(61,153,112)', # green
'rgb(40,35,35)', # black
'rgb(133,20,75)', # magenta
'rgb(255,65,54)', # red
'rgb(255,255,255)', # white
'rgb(255,220,0)'] # yellow
"rgb(0,116,217)", # blue
"rgb(35,205,205)", # cyan
"rgb(61,153,112)", # green
"rgb(40,35,35)", # black
"rgb(133,20,75)", # magenta
"rgb(255,65,54)", # red
"rgb(255,255,255)", # white
"rgb(255,220,0)",
] # yellow

for i in range(len(default_colors.keys())):
k = list(default_colors.keys())[i] # PY3 won't index keys
Expand All @@ -150,32 +197,34 @@ def set_axis_layout(self, axis_key, hide_labels):
:return (dict): An axis_key dictionary with set parameters.
"""
axis_defaults = {
'type': 'linear',
'ticks': 'outside',
'mirror': 'allticks',
'rangemode': 'tozero',
'showticklabels': True,
'zeroline': False,
'showgrid': False,
'showline': True,
}
"type": "linear",
"ticks": "outside",
"mirror": "allticks",
"rangemode": "tozero",
"showticklabels": True,
"zeroline": False,
"showgrid": False,
"showline": True,
}

if len(self.labels) != 0:
axis_key_labels = self.xaxis
if self.orientation in ['left', 'right']:
if self.orientation in ["left", "right"]:
axis_key_labels = self.yaxis
if axis_key_labels not in self.layout:
self.layout[axis_key_labels] = {}
self.layout[axis_key_labels]['tickvals'] = \
[zv*self.sign[axis_key] for zv in self.zero_vals]
self.layout[axis_key_labels]['ticktext'] = self.labels
self.layout[axis_key_labels]['tickmode'] = 'array'
self.layout[axis_key_labels]["tickvals"] = [
zv * self.sign[axis_key] for zv in self.zero_vals
]
self.layout[axis_key_labels]["ticktext"] = self.labels
self.layout[axis_key_labels]["tickmode"] = "array"

self.layout[axis_key].update(axis_defaults)

if hide_labels == True:
self.layout[axis_key].update({'showticklabels': False})
else: pass
self.layout[axis_key].update({"showticklabels": False})
else:
pass

return self.layout[axis_key]

Expand All @@ -191,24 +240,27 @@ def set_figure_layout(self, width, height, hide_labels):
:type hide_labels: boolean
:return: Plotly layout
"""
self.layout.update({
'showlegend': False,
'autosize': False,
'hovermode': 'closest',
'width': width,
'height': height
})
self.layout.update(
{
"showlegend": False,
"autosize": False,
"hovermode": "closest",
"width": width,
"height": height,
}
)

self.set_axis_layout(self.xaxis, hide_labels=hide_labels)
self.set_axis_layout(self.yaxis, hide_labels=False)

return self.layout


def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color_threshold):
def get_dendrogram_traces(
self, Z_dendrogram, hang, colorscale, hovertext, color_threshold
):
"""
Calculates all the elements needed for plotting a dendrogram.

:param Z_dendrogram: Matrix of observations as array of arrays
:type Z_dendrogram: ndarray
:param hang: dendrogram distance of leaf lines
Expand All @@ -218,28 +270,28 @@ def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color
:param hovertext: List of hovertext for constituent traces of dendrogram
:type hovertext: list
:return (tuple): Contains all the traces in the following order:

a. trace_list: List of Plotly trace objects for dendrogram tree
b. icoord: All X points of the dendrogram tree as array of arrays with length 4
c. dcoord: All Y points of the dendrogram tree as array of arrays with length 4
d. ordered_labels: leaf labels in the order they are going to appear on the plot
e. Z_dendrogram['leaves']: left-to-right traversal of the leaves
"""
icoord = scp.array(Z_dendrogram['icoord'])
dcoord = scp.array(Z_dendrogram['dcoord'])
ordered_labels = scp.array(Z_dendrogram['ivl'])
color_list = scp.array(Z_dendrogram['color_list'])
icoord = scp.array(Z_dendrogram["icoord"])
dcoord = scp.array(Z_dendrogram["dcoord"])
ordered_labels = scp.array(Z_dendrogram["ivl"])
color_list = scp.array(Z_dendrogram["color_list"])
colors = self.get_color_dict(colorscale)

trace_list = []

for i in range(len(icoord)):
if self.orientation in ['top', 'bottom']:
if self.orientation in ["top", "bottom"]:
xs = icoord[i]
else:
xs = dcoord[i]

if self.orientation in ['top', 'bottom']:
if self.orientation in ["top", "bottom"]:
ys = dcoord[i]
else:
ys = icoord[i]
Expand All @@ -264,28 +316,31 @@ def get_dendrogram_traces(self, Z_dendrogram, hang, colorscale, hovertext, color
y_coord.append(y)

trace = dict(
type='scattergl',
type="scattergl",
x=np.multiply(self.sign[self.xaxis], x_coord),
y=np.multiply(self.sign[self.yaxis], y_coord),
mode='lines',
marker=dict(color='rgb(40,35,35)'),
line=dict(color='rgb(40,35,35)', width=1), #dict(color=colors[color_key]),
mode="lines",
marker=dict(color="rgb(40,35,35)"),
line=dict(
color="rgb(40,35,35)", width=1
), # dict(color=colors[color_key]),
text=hovertext_label,
hoverinfo='text')
hoverinfo="text",
)

try:
x_index = int(self.xaxis[-1])
except ValueError:
x_index = ''
x_index = ""

try:
y_index = int(self.yaxis[-1])
except ValueError:
y_index = ''
y_index = ""

trace['xaxis'] = 'x' + x_index
trace['yaxis'] = 'y' + y_index
trace["xaxis"] = "x" + x_index
trace["yaxis"] = "y" + y_index

trace_list.append(trace)

return trace_list, icoord, dcoord, ordered_labels, Z_dendrogram['leaves']
return trace_list, icoord, dcoord, ordered_labels, Z_dendrogram["leaves"]
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