Webapp data and scripts#77
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MikeLippincott
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Jun 9, 2026
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LGTM. Ready to merge after addressing comments!
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| script_directory = pathlib.Path("../utils/").resolve() | ||
| sys.path.insert(0, str(script_directory)) | ||
| from data_loader import load_model_data, load_train_test_data |
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pointing out package anti-pattern here
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| features = combined_df[gene_cols] | ||
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| # In[8]: | ||
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| features |
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Consider merging these two into one cell and calling "head"
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| import random | ||
| import colorsys |
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| def generate_random_palette(num_colors, seed=12): | ||
| # Generate random colors with varied lightness and saturation | ||
| random.seed(seed) | ||
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| colors = [] | ||
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| for _ in range(num_colors): | ||
| h = random.random() # Random hue between 0 and 1 | ||
| l = random.uniform(0.2, 0.8) # Lightness between 0.3 and 0.9 for contrast | ||
| s = random.uniform(0.5, 1.0) # Saturation between 0.6 and 1.0 for vivid colors | ||
| color = colorsys.hls_to_rgb(h, l, s) # Convert HLS to RGB color | ||
| colors.append(color) | ||
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| return colors |
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Helper function might live better in the utils file, if not then consider moving to the top.
Add docstrings and type hints also
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| import plotly.graph_objects as go | ||
| import plotly.express as px | ||
| from sklearn.decomposition import PCA | ||
| from sklearn.preprocessing import StandardScaler |
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| # Step 2: Subset based on matching keys | ||
| subset_keys = ["model", "latent_dim_total", "init", "z"] |
| # In[18]: | ||
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| def generate_random_palette(num_colors, seed=12): |
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consider moving to top, adding type hints and adding docstrings
| # In[19]: | ||
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| def make_dropdown_pca_with_selection(df, title="PCA Interactive Plot"): |
| out = widgets.Output() # Create a fresh output for this plot! | ||
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| # Prepare PCA input | ||
| pca_input = df.drop(columns=["OncotreePrimaryDisease", "source", "ModelID"], errors="ignore").fillna(0) |
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fillna with - might not be the correct strategy here? TBD
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This has all of the data that should be necessary for the webapp, as well as a few shiny PCAs and the code for that.