From 5681b46d1aa1d7128877a3ec5fe1df26a14bfc19 Mon Sep 17 00:00:00 2001 From: bednarsky <72978444+bednarsky@users.noreply.github.com> Date: Tue, 19 Nov 2024 11:01:38 +0100 Subject: [PATCH] Avoid heatmap config default causing error --- config/config.yaml | 2 +- workflow/scripts/distance_matrix.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index fbdd365..9cdda6f 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -41,7 +41,7 @@ umap: 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 ##### LEIDEN ##### diff --git a/workflow/scripts/distance_matrix.py b/workflow/scripts/distance_matrix.py index 847b701..5188666 100644 --- a/workflow/scripts/distance_matrix.py +++ b/workflow/scripts/distance_matrix.py @@ -41,7 +41,8 @@ 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) + if n_observations < data.shape[0]: + data = data.sample(n=n_observations, random_state=42) # Convert DataFrame to NumPy array # data_np = data.to_numpy()