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Replace deprecated pertpy API usage #70

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Merged
Zethson merged 1 commit into from
Aug 4, 2026
Merged

Replace deprecated pertpy API usage #70

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2 changes: 1 addition & 1 deletion differential_gene_expression.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1229,7 +1229,7 @@
" This is the value to threshold on (commonly `< 0.05`).\n",
"- `contrast` — identifier of the contrast when multiple are tested at once; `None` here because we only ran one contrast.\n",
"\n",
"A standard summary is \"significantly differentially expressed\" = `adj_p_value < 0.05` **and** `|log_fc|` above some effect-size threshold (the volcano plot below uses `log2fc_thresh` for the latter).\n"
"A standard summary is \"significantly differentially expressed\" = `adj_p_value < 0.05` **and** `|log_fc|` above some effect-size threshold (the volcano plot below uses `log2fc_threshold` for the latter).\n"
]
},
{
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12 changes: 6 additions & 6 deletions mcfarland_use_case.ipynb
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Expand Up @@ -1827,10 +1827,10 @@
"edgr.plot_volcano(\n",
" lr_params,\n",
" log2fc_col=\"intercept\",\n",
" pvalue_col=\"intercept_pval_corrected\",\n",
" padj_col=\"intercept_pval_corrected\",\n",
" symbol_col=\"gene\",\n",
" pval_thresh=0.05,\n",
" log2fc_thresh=0.5,\n",
" padj_threshold=0.05,\n",
" log2fc_threshold=0.5,\n",
")"
]
},
Expand Down Expand Up @@ -1942,10 +1942,10 @@
"edgr.plot_volcano(\n",
" lr_params,\n",
" log2fc_col=\"slope\",\n",
" pvalue_col=\"slope_pval_corrected\",\n",
" padj_col=\"slope_pval_corrected\",\n",
" symbol_col=\"gene\",\n",
" pval_thresh=0.1,\n",
" log2fc_thresh=0.1,\n",
" padj_threshold=0.1,\n",
" log2fc_threshold=0.1,\n",
")"
]
},
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2 changes: 1 addition & 1 deletion milo.ipynb
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Expand Up @@ -2135,7 +2135,7 @@
"] ## notice how here logFCs are much smaller\n",
"\n",
"## Add COVID severity labels to mdata['milo'].obs\n",
"milo.add_covariate_to_nhoods_var(mdata, [\"COVID_severity\"])\n",
"milo.add_covariate_to_nhoods_obs(mdata, [\"COVID_severity\"])\n",
"mdata[\"milo\"].obs[\"COVID_severity\"] = (\n",
" mdata[\"milo\"].obs[\"COVID_severity\"].astype(\"category\").cat.reorder_categories(severity_order)\n",
")\n",
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