17821832757

Committed 18 Sep 2025 07:46AM UTC coverage: 20.461% (+1.8%) from 18.666%

Build # 17821832757

Build Type

push

github

Committed by

Nicholas-Freitas

Commit Message

Merge remote-tracking branch 'origin/freitas_refactor_5_16_25' into main

Coverage Stats

0 of 634 new or added lines in 6 files covered. (0.0%)

2 existing lines in 1 file now uncovered.

470 of 2297 relevant lines covered (20.46%)

0.82 hits per line

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0.0

/src/htbam_analysis/analysis/plot.py

NEW 1	from dash import Dash, dcc, html, Input, Output, no_update, State	×
NEW 2	import plotly.graph_objs as go	×
NEW 3	import base64	×
NEW 4	import tempfile	×
NEW 5	import matplotlib.pyplot as plt	×
NEW 6	import numpy as np	×
7
NEW 8	def plot_chip(plotting_var, chamber_names, graphing_function=None, title=None):	×
9	''' This function creates a Dash visualization of a chip, based on a certain Run (run_name)
10	Inputs:
11	plotting_var: a dictionary mapping chamber_id to the variable to be plotted for that chamber
12	chamber_names: a dictionary mapping chamber_id to the name of the sample in the chamber (e.g. '1,1': ecADK_XYZ')
13	graphing_function: a function that takes in a single chamber_id (e.g. '1,1') and matplotlib axis and returns the axis object after plotting.
14	title: a string to be used as the title of the plot
15	TODO: make all the variables stored in Dash properly...
16	'''
17
18	# Make the image array
19	#NB: eventually, store width/height in DB and reference!
NEW 20	img_array = np.zeros([56,32])	×
21
22	# Here we're plotting to value for each chamber (e.g. coloring by std curve slope)
NEW 23	for chamber_id, value in plotting_var.items():	×
NEW 24	x = int(chamber_id.split(',')[0])	×
NEW 25	y = int(chamber_id.split(',')[1])	×
NEW 26	img_array[y-1,x-1] = value	×
27
28	#generate title
NEW 29	if title is None:	×
NEW 30	title = ''	×
31
32	#Create the figure
NEW 33	layout = go.Layout()	×
34
35	# create 1‐indexed axes
NEW 36	x_vals = list(range(1, img_array.shape[1] + 1))	×
NEW 37	y_vals = list(range(1, img_array.shape[0] + 1))	×
38
NEW 39	heatmap = go.Heatmap(	×
40	x=x_vals,
41	y=y_vals,
42	z=img_array,
43	colorscale='Viridis',
44	hovertemplate='x=%{x}<br>y=%{y}<br>z=%{z}<extra></extra>'
45	)
46
NEW 47	fig = go.Figure(layout=layout, data=heatmap)	×
48
49	#center title in fig
NEW 50	fig.update_layout(title=title,	×
51	title_x=0.5,
52	yaxis=dict(scaleanchor="x", scaleratio=1, autorange='reversed'),
53	xaxis=dict(scaleratio=1),
54	plot_bgcolor='rgba(0,0,0,0)',
55	width=600, height=600,
56	hovermode='x')
NEW 57	fig.update_xaxes(showticklabels=False)	×
NEW 58	fig.update_yaxes(showticklabels=False)	×
59
60	#create dash app:
NEW 61	app = Dash(__name__)	×
NEW 62	app.layout = html.Div(	×
63	style={'display': 'flex'},
64	children=[
65	html.Div(
66	style={'flex': '1'},
67	children=[
68	dcc.Graph(id="graph", figure=fig, clear_on_unhover=True),
69	dcc.Tooltip(id="graph-tooltip"),
70	]
71	),
72	html.Div(id="side-panel", style={'flex': '1', 'paddingLeft': '20px', 'backgroundColor': 'white'}) # Set side-panel background to white
73	]
74	)
75
76	### GRAPHING FUNCTION ON HOVER:
NEW 77	if graphing_function is not None:	×
NEW 78	@app.callback(	×
79	Output("graph-tooltip", "show"),
80	Output("graph-tooltip", "bbox"),
81	Output("graph-tooltip", "children"),
82	Input("graph", "hoverData"),
83	)
NEW 84	def display_hover(hoverData):	×
NEW 85	if hoverData is None:	×
NEW 86	return False, no_update, no_update	×
87	# demo only shows the first point, but other points may also be available
NEW 88	pt = hoverData["points"][0]	×
NEW 89	chamber_id = str(pt['x']) + ',' + str(pt['y'])	×
NEW 90	bbox = pt["bbox"]	×
NEW 91	chamber_name = chamber_names[chamber_id]	×
92	#get the data for the point:
NEW 93	fig, ax = plt.subplots()	×
NEW 94	ax = graphing_function(chamber_id, ax)	×
95	#reduce whitespace on margins of graph:
NEW 96	fig.subplots_adjust(left=0.1, bottom=0.1, right=0.9, top=0.9, wspace=0, hspace=0)	×
97	#save the figure as a temp file:
NEW 98	tempfile_name = tempfile.NamedTemporaryFile().name+'.png'	×
NEW 99	plt.savefig(tempfile_name)	×
NEW 100	plt.close()	×
101	# #read in temp file as base64 encoded string:
NEW 102	with open(tempfile_name, "rb") as image_file:	×
NEW 103	img_src = "data:image/png;base64," + str(base64.b64encode(image_file.read()).decode("utf-8"))	×
NEW 104	children = [	×
105	html.Div(children=[
106	#no space after header:
107	html.H3('{},{}: {}'.format(pt['x'], pt['y'], chamber_name), style={"color": 'black', "fontFamily":"Arial", "textAlign": "center", "marginBottom": "0px"}), #1-index
108	#add the image with reduced whitespace:
109	html.Img(src=img_src, style={"width": "100%"}),
110	],
111	style={'width': '400px', 'white-space': 'none'})
112	]
113
NEW 114	return True, bbox, children	×
115
116	### HIGHLIGHT ON HOVER / CLICK ###
NEW 117	@app.callback(	×
118	Output("graph", "figure"),
119	Input("graph", "hoverData"),
120	Input("graph", "clickData"),
121	State("graph", "figure"),
122	)
NEW 123	def update_highlights(hoverData, clickData, fig):	×
124	# clear old shapes
NEW 125	fig["layout"]["shapes"] = []	×
126
127	# hover => red outlines
NEW 128	if hoverData:	×
NEW 129	pt = hoverData["points"][0]	×
NEW 130	sample = chamber_names.get(f"{pt['x']},{pt['y']}")	×
NEW 131	if sample:	×
NEW 132	for cid, name in chamber_names.items():	×
NEW 133	if name == sample:	×
NEW 134	i, j = map(int, cid.split(","))	×
NEW 135	fig["layout"]["shapes"].append({	×
136	"type": "rect",
137	"x0": i-0.4, "x1": i+0.4,
138	"y0": j-0.4, "y1": j+0.4,
139	"line": {"color": "red", "width": 2},
140	"fillcolor": "rgba(0,0,0,0)",
141	"name": "hover"
142	})
143
144	# click => magenta outlines
NEW 145	if clickData:	×
NEW 146	pt = clickData["points"][0]	×
NEW 147	sample = chamber_names.get(f"{pt['x']},{pt['y']}")	×
NEW 148	if sample:	×
NEW 149	for cid, name in chamber_names.items():	×
NEW 150	if name == sample:	×
NEW 151	i, j = map(int, cid.split(","))	×
NEW 152	fig["layout"]["shapes"].append({	×
153	"type": "rect",
154	"x0": i-0.4, "x1": i+0.4,
155	"y0": j-0.4, "y1": j+0.4,
156	"line": {"color": "magenta", "width": 3},
157	"fillcolor": "rgba(0,0,0,0)",
158	"name": "selected"
159	})
160
NEW 161	return fig	×
162
163	### GRAPHING FUNCTION ON CLICK (side‐panel) ###
NEW 164	if graphing_function is not None:	×
NEW 165	@app.callback(	×
166	Output("side-panel", "children"),
167	Input("graph", "clickData"),
168	)
NEW 169	def display_click_side(clickData):	×
NEW 170	if clickData is None:	×
NEW 171	return no_update	×
172	# identify clicked chamber
NEW 173	pt = clickData["points"][0]	×
NEW 174	cid = f"{pt['x']},{pt['y']}"	×
NEW 175	sample = chamber_names.get(cid, "")	×
176
177	# generate inset plot PNG
NEW 178	fig2, ax2 = plt.subplots()	×
NEW 179	ax2 = graphing_function(cid, ax2)	×
NEW 180	fig2.subplots_adjust(left=0.1, bottom=0.1, right=0.9, top=0.9)	×
NEW 181	tmp = tempfile.NamedTemporaryFile().name + ".png"	×
NEW 182	plt.savefig(tmp)	×
NEW 183	plt.close(fig2)	×
NEW 184	with open(tmp, "rb") as f:	×
NEW 185	img_src = "data:image/png;base64," + base64.b64encode(f.read()).decode("utf-8")	×
186
187	# return side‐panel contents
NEW 188	return html.Div([	×
189	html.H3(f"{cid}: {sample}", style={"textAlign": "center"}),
190	html.Img(src=img_src, style={"width": "100%"})
191	])
192
NEW 193	app.run_server()	×

pinneylab / htbam_analysis / 17821832757

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