diff --git a/sincei/_deprecated.py b/sincei/_deprecated.py index 05cebfc..c113476 100644 --- a/sincei/_deprecated.py +++ b/sincei/_deprecated.py @@ -135,6 +135,7 @@ def cluster_LSA( Graph object. """ import community + # cluster on cel-topic dist _distances = pairwise_distances(cell_topic.iloc[:, 1:], metric=distance_metric) knn_indices, knn_distances = _get_indices_distances_from_dense_matrix(_distances, nk) diff --git a/sincei/scCountReads.py b/sincei/scCountReads.py index 7e78e2a..9fc4f49 100755 --- a/sincei/scCountReads.py +++ b/sincei/scCountReads.py @@ -200,11 +200,11 @@ def main(args=None): num_reads_per_bin, regionList = c.run(allArgs=args) - sys.stderr.write("Number of bins " "found: {}\n".format(num_reads_per_bin.shape[0])) + sys.stderr.write("Number of bins/features " "found: {}\n".format(num_reads_per_bin.shape[0])) if num_reads_per_bin.shape[0] < 1: exit( - "ERROR: too few non zero bins found.\n" + "ERROR: too few non zero bins/features found.\n" "If using --region please check that this " "region is covered by reads.\n" )