def display_hover_image(index):
if index is None:
return ''
smiles = details.iloc[index]['SMILES']
image = smiles_to_image(smiles, png=True, b64=True, crop=True, size=500)
src = 'data:image/png;base64, %s' % image
return src
def get_image_src(cid):
if cid is None:
return ''
smiles = details.loc[cid, 'SMILES']
image = smiles_to_image(smiles, png=True, b64=True, crop=True, size=250)
src = 'data:image/png;base64, %s' % image
return src
def hover_fn(trace, points, state):
#print(points)
try:
ind = points.point_inds[0]
if trace.name == 'Possible Molecules':
use = big_umap
else:
use = known_umap
smiles = use.index[ind]
image_widget.value = smiles_to_image(smiles, size=200)
text_widget.value = smiles
except IndexError:
pass
except Exception as e:
print(e)
def plot(big_umap, known_umap, skip=10):
big_umap = big_umap.iloc[::skip]
known_umap = known_umap.iloc[::skip]
# The GDB scatter plot
skip = 10
big_scatter = go.Scatter(
x=big_umap.loc[:, 0],
y=big_umap.loc[:, 1],
name='Possible Molecules',
mode="markers",
hoverinfo="text",
opacity=0.5,
marker={
"size": 5,
"line": {
"width": 0.5,
"color": "white"
},
"color": big_umap.loc[:, 'p'],
"colorscale": 'magma',
"colorbar": {
'thickness': 20,
'title': 'p(Odorous)'
},
},
)
# The known odorants scatter plot
known_scatter = go.Scattergl(
x=known_umap.loc[:, 0],
y=known_umap.loc[:, 1],
name='Known Odorous',
mode="markers",
hoverinfo="text",
opacity=1,
marker={
"size": 5,
"line": {
"width": 0.5,
"color": "white"
},
"color": "blue",
},
)
# The axes, etc.
layout = go.Layout(xaxis={
"type": "linear",
"title": "",
"showline": False,
"showticklabels": False
},
yaxis={
"type": "linear",
"title": "",
"showline": False,
"showticklabels": False
},
margin={
"l": 40,
"b": 40,
"t": 10,
"r": 10
},
legend={
"x": 0,
"y": 1,
'font': {
'size': 15,
'color': 'white'
}
},
hovermode="closest",
paper_bgcolor="rgba(0,0,0,0)",
plot_bgcolor="rgba(10,10,10,1)",
width=1000,
height=1000,
xaxis_showgrid=False,
yaxis_showgrid=False,
xaxis_zeroline=False,
yaxis_zeroline=False)
fig = go.FigureWidget(data=[big_scatter, known_scatter], layout=layout)
fig.layout.hovermode = 'closest'
# The 2D drawing of the molecule
first_smiles = "CCCCO"
image_widget = Image(value=smiles_to_image(first_smiles),
layout=Layout(height="200px",
width="200px",
left='50px',
top='-250px'))
text_widget = Text(value=first_smiles,
placeholder=first_smiles,
description='SMILES:',
disabled=False,
layout=Layout(width='400px', left='25px', top='-285px'))
def hover_fn(trace, points, state):
#print(points)
try:
ind = points.point_inds[0]
if trace.name == 'Possible Molecules':
use = big_umap
else:
use = known_umap
smiles = use.index[ind]
image_widget.value = smiles_to_image(smiles, size=200)
text_widget.value = smiles
except IndexError:
pass
except Exception as e:
print(e)
def click_fn(trace, points, state):
global hover_on
if hover_on:
fig.data[0].on_hover(None)
hover_on = 0
else:
fig.data[0].on_hover(hover_fn)
hover_on = 1
fig.data[0].on_hover(hover_fn)
fig.data[0].on_click(click_fn)
canvas = GridBox([fig, image_widget, text_widget], layout={'gridgap': '0'})
return canvas
def plotly_embedding(embedding, features=None, show_features=None, colors=None, colorscale='rainbow'):
"""
params:
embedding: A dataframe wrapped around e.g. a fitted TSNE object, with an index of CIDs
features: A dataframe of features, e.g. names, SMILES strings, or physicochemical features,
with an index of CIDs
"""
if features is None:
features = pyrfume.load_data("odorants/all-cids-properties.csv", usecols=range(5))
# Only retain those rows corresponding to odorants in the embedding
features = features.loc[embedding.index]
show_features = show_features or list(features)
def format_features(col):
return "%s: %s" % (index_name, col.values.split('<br>'))
try:
index_name = features.index.name or 'Index'
names = (
features.loc[:, show_features]
.reset_index()
.astype("str")
.apply(format_features, axis=1)
)
except Exception:
names = features.index
assert embedding.shape[0] == features.shape[0]
# The scatter plot
scatter = go.Scatter(
x=embedding.iloc[:, 0],
y=embedding.iloc[:, 1],
text=names,
mode="markers",
hoverinfo="text",
opacity=0.5,
marker={
"size": 5,
"line": {"width": 0.5, "color": "white"},
"color": colors if colors is not None else "black",
"colorscale": colorscale,
},
)
# The axes, etc.
layout = go.Layout(
xaxis={"type": "linear", "title": "", "showline": False, "showticklabels": False},
yaxis={"type": "linear", "title": "", "showline": False, "showticklabels": False},
margin={"l": 40, "b": 40, "t": 10, "r": 10},
legend={"x": 0, "y": 1},
hovermode="closest",
paper_bgcolor="rgba(0,0,0,0)",
plot_bgcolor="rgba(0,0,0,0)",
width=500,
height=500,
)
fig = go.FigureWidget(data=[scatter], layout=layout)
fig.layout.hovermode = 'closest'
# The 2D drawing of the molecule
image_widget = Image(
value=smiles_to_image("CCCCO"), layout=Layout(height="300px", width="300px")
)
def hover_fn(trace, points, state):
ind = points.point_inds[0]
smiles = features["SMILES"].iloc[ind]
image_widget.value = smiles_to_image(smiles)
scatter = fig.data[0]
scatter.on_hover(hover_fn)
canvas = VBox([fig, image_widget])
return canvas
def hover_fn(trace, points, state):
ind = points.point_inds[0]
smiles = features["SMILES"].iloc[ind]
image_widget.value = smiles_to_image(smiles)
def get_image_src(smiles):
if not smiles:
return ''
image = smiles_to_image(smiles, png=True, b64=True, crop=True, size=250)
src = 'data:image/png;base64, %s' % image
return src