From 07e5f138f0249a6fbf8be8d79146b902e573d2b9 Mon Sep 17 00:00:00 2001 From: Luis Alonso Esteban Date: Tue, 12 Nov 2024 16:12:47 +0100 Subject: [PATCH] Microclustering deprecation errors fixed --- compass/compass/microclustering.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/compass/compass/microclustering.py b/compass/compass/microclustering.py index b49a9bf..7e50403 100644 --- a/compass/compass/microclustering.py +++ b/compass/compass/microclustering.py @@ -98,8 +98,8 @@ def filterGenesThreshold(data, threshold): def filterGenesFano(data, num_mad=2): #Could sample columns at random to improve runtime - mu = data.mean(axis=1).ravel() - fano = data.var(axis=1).ravel() / mu + mu = data.mean(axis=1).to_numpy() + fano = data.var(axis=1).to_numpy() / mu mu_argsort = np.argsort(mu) mu_sort = mu[mu_argsort] @@ -178,7 +178,7 @@ def pool_matrix_cols(data, pools): for i in pools[g]: groups[data.columns[i]] = g groups = pd.DataFrame.from_dict(groups, orient='index', columns=['compass_microcluster']).T - return data.append(groups).T.groupby("compass_microcluster").mean().T.rename(mapper=lambda x: 'cluster_'+str(int(x)), axis=1) + return pd.concat([data, groups]).T.groupby("compass_microcluster").mean().T.rename(mapper=lambda x: 'cluster_'+str(int(x)), axis=1) def unpool_columns(pooled_data, pools, data): unpooled_cols = []