clearer error message in QC

README.md

@@ -22,7 +22,7 @@
 2. [`profile`](https://pinellolab.github.io/crispr-bean/profile.html): Profile editing preferences of your editor.  
 3. [`qc`](https://pinellolab.github.io/crispr-bean/qc.html): Quality control report and filtering out / masking of aberrant sample and guides  
 4. [`filter`](https://pinellolab.github.io/crispr-bean/filter.html): Filter reporter alleles; essential for `tiling` mode that allows for all alleles generated from gRNA.
-5. [`run`](https://pinellolab.github.io/crispr-bean/run.html): Quantify targeted variants' effect sizes from screen data. **See more about the [model](https://pinellolab.github.io/crispr-bean/model.html) & [output](https://github.com/pinellolab/crispr-bean/tree/main/docs/example_run_output)**
+5. [`run`](https://pinellolab.github.io/crispr-bean/run.html): Quantify targeted variants' effect sizes from screen data. **See more about the [model](https://pinellolab.github.io/crispr-bean/model.html) & [output](https://pinellolab.github.io/crispr-bean/run.html#output)**
 * Screen data is saved as [`ReporterScreen` object](https://pinellolab.github.io/crispr-bean/reporterscreen.html) in the pipeline.
 BEAN stores mapped gRNA and allele counts in `ReporterScreen` object which is compatible with [AnnData](https://anndata.readthedocs.io/en/latest/index.html). 
 

bean/notebooks/sample_quality_report.ipynb

@@ -262,17 +262,24 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ax = pt.qc.plot_lfc_correlation(\n",
-    "    bdata,\n",
-    "    selected_guides,\n",
-    "    method=\"Spearman\",\n",
-    "    cond1=comp_cond1,\n",
-    "    cond2=comp_cond2,\n",
-    "    rep_col=replicate_label,\n",
-    "    compare_col=condition_label,\n",
-    "    figsize=(10, 10),\n",
-    ")\n",
-    "\n",
+    "try:\n",
+    "    ax = pt.qc.plot_lfc_correlation(\n",
+    "        bdata,\n",
+    "        selected_guides,\n",
+    "        method=\"Spearman\",\n",
+    "        cond1=comp_cond1,\n",
+    "        cond2=comp_cond2,\n",
+    "        rep_col=replicate_label,\n",
+    "        compare_col=condition_label,\n",
+    "        figsize=(10, 10),\n",
+    "    )\n",
+    "except ValueError as e:\n",
+    "    if \"rep_col\" in str(e):\n",
+    "        raise ValueError(f\"Column `{replicate_label}` fed in with `--replicate-col {replicate_label}` does not exist in the input .h5ad file. Please check your input.\") from e\n",
+    "    elif \"compare_col\" in str(e):\n",
+    "        raise ValueError(f\"Column `{condition_label}` fed in with `--condition-col {condition_label}` does not exist in the input .h5ad file. Please check your input.\") from e\n",
+    "    elif \"cond1\" in str(e):\n",
+    "        raise ValueError(f\"Samples with `{condition_label}` value of `{comp_cond1}` or `{comp_cond2}` does not exist. Check your input argument fed in with `--lfc-conds `{comp_cond1},{comp_cond2}`.\")\n",
     "ax.set_title(\"top/bot LFC correlation, Spearman\")\n",
     "plt.yticks(rotation=0)\n",
     "plt.xticks(rotation=90)\n",