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distance_matrix.py - avoid that config:heatmap:n_observations default causes error #58

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bednarsky opened this issue Nov 15, 2024 · 1 comment · May be fixed by #63
Open

distance_matrix.py - avoid that config:heatmap:n_observations default causes error #58

bednarsky opened this issue Nov 15, 2024 · 1 comment · May be fixed by #63
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enhancement New feature or request

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@bednarsky
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  • I ran the unsupervised analysis leaving many of the default parameters unchanged
  • One of them causes an error for my pseudobulks with less that that number of cells
heatmap:
    metrics: ['correlation','cosine']
    hclust_methods: ['complete']
-    n_observations: 1000 # random sampled proportion float (0-1] or absolute number as integer
+    n_observations: 1 # random sampled proportion float (0-1] or absolute number as integer
    n_features: 0.5 # highly variable features proportion float (0-1] or absolute number as integer
  • alternative could also be to make the respective line defensive

    unsupervised_analysis/workflow/scripts/distance_matrix.py

    Lines 40 to 44 in f902eff

    # downsample observations
    if data_or_feature == "observations":
    if isinstance(n_observations, float) or n_observations==1:
    n_observations = int(math.floor(n_observations * data.shape[0]))
    data = data.sample(n=n_observations, random_state=42) 
# downsample observations
if data_or_feature == "observations":
     if isinstance(n_observations, float) or n_observations==1:
        n_observations = int(math.floor(n_observations * data.shape[0]))
+    if n_observations < data.shape[0]:
        data = data.sample(n=n_observations, random_state=42)
@bednarsky bednarsky changed the title Improve heatmap: n_observations default to avoid potential error Improve heatmap: avoid that n_observations default causes error Nov 16, 2024
@bednarsky bednarsky changed the title Improve heatmap: avoid that n_observations default causes error heatmap: avoid that n_observations default causes error Nov 16, 2024
@bednarsky bednarsky changed the title heatmap: avoid that n_observations default causes error distance_matrix.py - avoid that config:heatmap:n_observations default causes error Nov 16, 2024
@sreichl
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sreichl commented Nov 18, 2024

both changes make sense, feel free to PR if tested.

@sreichl sreichl added the enhancement New feature or request label Nov 18, 2024
@bednarsky bednarsky linked a pull request Nov 19, 2024 that will close this issue
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Avoid heatmap config default causing error bednarsky/unsupervised_analysis
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@sreichl @bednarsky