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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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heatmap_dotplot() in the development branch #239

Closed pchiang5 closed 8 months ago

pchiang5 commented 8 months ago

Describe the bug I used the scenicplus in the development branch to generate the mdata_r with the structure below. However, it showed errors whatever I input ('size_val,' 'col_val'...) with the sort_data_by parameter. What shall be the correct str for plotting? Thank you.

In [5]: mdata_r Out[5]: MuData object with n_obs × n_vars = 5525 × 374671 backed at '/mnt/c/Users/pc/Downloads/scenicplus/tests/test_cli/scplusmdata.h5mu' uns: 'direct_e_regulon_metadata', 'extended_e_regulon_metadata' 6 modalities scRNA_counts: 5525 x 33866 obs: 'batch', 'species', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', '_scvi_batch', '_scvi_labels', 'leiden', 'celltype' var: 'species', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts' obsm: 'X_scVI', 'X_umap', '_scvi_extra_continuous_covs' scATAC_counts: 5525 x 340585 obs: 'cisTopic_nr_acc', 'cisTopic_log_nr_acc', 'Dupl_nr_frag', 'barcode', 'Log_unique_nr_frag', 'cisTopic_nr_frag', 'Total_nr_frag_in_regions', 'cisTopic_log_nr_frag', 'FRIP', 'Total_nr_frag', 'Dupl_rate', 'Unique_nr_frag', 'TSS_enrichment', 'Unique_nr_frag_in_regions', 'Log_total_nr_frag', 'batch', 'species', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', '_scvi_batch', '_scvi_labels', 'leiden', 'celltype', 'sample_id' var: 'Chromosome', 'Start', 'End', 'Width', 'cisTopic_nr_frag', 'cisTopic_log_nr_frag', 'cisTopic_nr_acc', 'cisTopic_log_nr_acc' direct_gene_based_AUC: 5525 x 69 direct_region_based_AUC: 5525 x 69 extended_gene_based_AUC: 5525 x 41 extended_region_based_AUC: 5525 x 41

To Reproduce

heatmap_dotplot(
scplus_mudata = mdata_r,
size_modality = 'direct_region_based_AUC', #specify what to plot as dot sizes, target region enrichment in this case
color_modality = 'scRNA_counts', #specify  what to plot as colors, TF expression in this case
group_variable= 'scRNA_counts:celltype',
eRegulon_metadata_key = 'direct_e_regulon_metadata',
size_feature_key = 'Region_signature_name',
color_feature_key = 'Gene',
feature_name_key = 'eRegulon_name',
sort_data_by= "color_variable" )

Error output

In [4]: heatmap_dotplot( ...: scplus_mudata = mdata_r, ...: size_modality = 'direct_region_based_AUC', #specify what to plot as dot sizes, target region enrichment in this case ...: color_modality = 'scRNA_counts', #specify what to plot as colors, TF expression in this case ...: group_variable= 'scRNA_counts:celltype', ...: eRegulon_metadata_key = 'direct_e_regulon_metadata', ...: size_feature_key = 'Region_signature_name', ...: color_feature_key = 'Gene', ...: feature_name_key = 'eRegulon_name', ...: sort_data_by= "color_variable" ) ...: ^[[A/home/pc/miniconda3/envs/scenicplusdev/lib/python3.8/site-packages/scenicplus/plotting/dotplot.py:42: FutureWarning: The default value of numeric_only in DataFrameGroupBy.mean is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function. Empty DataFrame Columns: [scRNA_counts, scRNA_counts:celltype, direct_region_based_AUC, eRegulon_name] Index: []

KeyError Traceback (most recent call last) Cell In[4], line 1 ----> 1 heatmap_dotplot( 2 scplus_mudata = mdata_r, 3 size_modality = 'direct_region_based_AUC', #specify what to plot as dot sizes, target region enrichment in this case 4 color_modality = 'scRNA_counts', #specify what to plot as colors, TF expression in this case 5 group_variable= 'scRNA_counts:celltype', 6 eRegulon_metadata_key = 'direct_e_regulon_metadata', 7 size_feature_key = 'Region_signature_name', 8 color_feature_key = 'Gene', 9 feature_name_key = 'eRegulon_name', 10 sort_data_by= "color_variable" )

File /home/pc/miniconda3/envs/scenicplusdev/lib/python3.8/site-packages/scenicplus/plotting/dotplot.py:117, in heatmap_dotplot(scplus_mudata, size_modality, color_modality, group_variable, eRegulon_metadata_key, size_feature_key, color_feature_key, feature_name_key, sort_data_by, subset_feature_names, scale_size_matrix, scale_color_matrix, group_variable_order, save, figsize, split_repressor_activator, orientation) 115 else: 116 plotting_df[group_variable] = pd.Categorical(plotting_df[group_variable], categories=group_variable_order) --> 117 tmp = plotting_df[[group_variable, feature_name_key, sort_data_by]] \ 118 .pivot_table(index=group_variable, columns=feature_name_key) \ 119 .fillna(0)[sort_data_by] 120 if group_variable_order is not None: 121 tmp = tmp.loc[group_variable_order]

File /home/pc/miniconda3/envs/scenicplusdev/lib/python3.8/site-packages/pandas/core/frame.py:3811, in DataFrame.getitem(self, key) 3809 if is_iterator(key): 3810 key = list(key) -> 3811 indexer = self.columns._get_indexer_strict(key, "columns")[1] 3813 # take() does not accept boolean indexers 3814 if getattr(indexer, "dtype", None) == bool:

File /home/pc/miniconda3/envs/scenicplusdev/lib/python3.8/site-packages/pandas/core/indexes/base.py:6108, in Index._get_indexer_strict(self, key, axis_name) 6105 else: 6106 keyarr, indexer, new_indexer = self._reindex_non_unique(keyarr) -> 6108 self._raise_if_missing(keyarr, indexer, axis_name) 6110 keyarr = self.take(indexer) 6111 if isinstance(key, Index): 6112 # GH 42790 - Preserve name from an Index

File /home/pc/miniconda3/envs/scenicplusdev/lib/python3.8/site-packages/pandas/core/indexes/base.py:6171, in Index._raise_if_missing(self, key, indexer, axis_name) 6168 raise KeyError(f"None of [{key}] are in the [{axis_name}]") 6170 not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique()) -> 6171 raise KeyError(f"{not_found} not in index")

KeyError: "['color_variable'] not in index"

Expected behavior the heatmap jumps out like with the tutorial.

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pchiang5 commented 8 months ago

It was caused by the incompatibility of the sparse format in the RNA matrix.