InvalidIndexError: (slice(None, None, None), 30751) while using coverage plot

[yojetsharma]

genes_violin_plot = 'MAFIP'
region='chr9:39287963-39288463'
# Create a coverage plot
fig = coverage_plot(
    SCENICPLUS_obj=scplus_obj,  # Your SCENICPLUS object
    bw_dict=bw_dict,
    region=region,
    genes_violin_plot=genes_violin_plot,
    gene_height=1,
    exon_height=4,
    meta_data_key='broader_annotation',  # Adjust based on your metadata structure
    figsize=(8, 10)  # Adjust figure size as needed
)
scplus_obj.gene_names:
Index(['MIR1302-2HG', 'AL627309.1', 'AL627309.5', 'AL627309.4', 'AP006222.2',
       'AL669831.2', 'LINC01409', 'FAM87B', 'LINC01128', 'LINC00115',
       ...
       'MAFIP', 'AC011043.1', 'AC011043.2', 'AC011841.1', 'AL354822.1',
       'AL592183.1', 'AC240274.1', 'AC004556.3', 'AC007325.4', 'AC007325.2'],
      dtype='object', length=30761)

[SeppeDeWinter]

Hi @yojetsharma

Can you provide the full error output please?

All the best,

Seppe

[yojetsharma]

The code in question was run using a different pr_annotation file (i will get back to you on that complete shortly). But the code I tried recently gave the following error (pr_annotation file was the same that is used for pycistopic analysis for this):

from scenicplus.plotting.coverageplot import coverage_plot
scenicplus.plotting.coverageplot.coverage_plot(
    scplus_obj,
    bw_dict=bw_dict,
    region='chr14:100725892-100739224',
    meta_data_key='broader_annotation',
    pr_consensus_bed=pr_consensus_bed,
    pr_gtf=pr_annotation,
    genes_violin_plot='DLK1'
)

/home/praghu/yojetsharma/.conda/envs/scenicplus/lib/python3.11/site-packages/pyranges/methods/intersection.py:52: FutureWarning: In a future version, df.iloc[:, i] = newvals will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either df[df.columns[i]] = newvals or, if columns are non-unique, df.isetitem(i, newvals) scdf.loc[:, "Start"] = new_starts /home/praghu/yojetsharma/.conda/envs/scenicplus/lib/python3.11/site-packages/pyranges/methods/intersection.py:53: FutureWarning: In a future version, df.iloc[:, i] = newvals will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either df[df.columns[i]] = newvals or, if columns are non-unique, df.isetitem(i, newvals) scdf.loc[:, "End"] = new_ends

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[75], line 2
      1 from scenicplus.plotting.coverageplot import coverage_plot
----> 2 scenicplus.plotting.coverageplot.coverage_plot(
      3     scplus_obj,
      4     bw_dict=bw_dict,
      5     region='chr14:100725892-100739224',
      6     meta_data_key='broader_annotation',
      7     pr_consensus_bed=pr_consensus_bed,
      8     pr_gtf=pr_annotation,
      9     genes_violin_plot='DLK1'
     10 )

File ~/.conda/envs/scenicplus/lib/python3.11/site-packages/scenicplus/plotting/coverageplot.py:288, in coverage_plot(SCENICPLUS_obj, bw_dict, region, genes_violin_plot, genes_arcs, gene_height, exon_height, meta_data_key, pr_consensus_bed, region_bed_height, pr_gtf, pr_interact, bw_ymax, color_dict, cmap, plot_order, figsize, fontsize_dict, gene_label_offset, arc_rad, arc_lw, cmap_violinplots, violinplots_means_color, violinplots_edge_color, violoinplots_alpha, width_ratios_dict, height_ratios_dict, sort_vln_plots, add_custom_ax)
    283 gtf_region_intersect = pr_gtf.intersect(pr_region)
    284 # only keep exon and gene info
    285 gtf_region_intersect = gtf_region_intersect[np.logical_and(
    286     np.logical_or(gtf_region_intersect.Feature == 'gene',
    287                   gtf_region_intersect.Feature == 'exon'),
--> 288     gtf_region_intersect.gene_type == 'protein_coding')]
    289 # iterate over all genes in intersect
    290 ax = axs_bw[subplot_idx]

File ~/.conda/envs/scenicplus/lib/python3.11/site-packages/pyranges/pyranges.py:269, in PyRanges.__getattr__(self, name)
    244 """Return column.
    245 
    246 Parameters
   (...)
    264 Name: Start, dtype: int32
    265 """
    267 from pyranges.methods.attr import _getattr
--> 269 return _getattr(self, name)

File ~/.conda/envs/scenicplus/lib/python3.11/site-packages/pyranges/methods/attr.py:67, in _getattr(self, name)
     65     return pd.concat([df[name] for df in self.values()])
     66 else:
---> 67     raise AttributeError("PyRanges object has no attribute", name)

AttributeError: ('PyRanges object has no attribute', 'gene_type')