KeyError: 'cell' when running dimentionality reducition Bug report [BUG]

[degrainger]

Describe the bug Unable to run dimensionality reduction (run_umap() or run_tsne() on my cistopic object.

To Reproduce

# Load cisTopic object
import pickle
infile = open(outDir + 'cistopic_obj_filtered.pkl', 'rb')
cistopic_obj = pickle.load(infile)
infile.close()

from pycisTopic.clust_vis import (
    find_clusters,
    run_umap,
    run_tsne,
    plot_metadata,
    plot_topic,
    cell_topic_heatmap
)

run_umap(
    cistopic_obj,
    target  = 'cell', scale=True)

Error output

2024-05-17 10:10:36,400 cisTopic INFO Running UMAP

KeyError Traceback (most recent call last) Cell In[7], line 1 ----> 1 run_umap( 2 cistopic_obj, 3 target = 'cell', scale=True)

File ~/pycisTopic/src/pycisTopic/clust_vis.py:249, in run_umap(cistopic_obj, target, scale, reduction_name, random_state, selected_topics, selected_features, harmony, rna_components, rna_weight, **kwargs) 247 dr = pd.DataFrame(embedding, index=data_names, columns=["UMAP_1", "UMAP_2"]) 248 if target == "cell": --> 249 cistopic_obj.projections["cell"][reduction_name] = dr 250 if target == "region": 251 cistopic_obj.projections["region"][reduction_name] = dr

KeyError: 'cell'

Expected behavior UMAP to be calculated for my object

Version (please complete the following information):

• Python 3.11.9
• pycisTopic 2.0a0

[SeppeDeWinter]

Hi @degrainger

Does

cistopic_obj.projections["cell"] = {}

Before running the function fix your issue?

Best,

Seppe

[degrainger]

Thanks very much @SeppeDeWinter, that worked a treat! Best wishes, Dave