diff --git a/figure-5-comparative-analysis.ipynb b/figure-5-comparative-analysis.ipynb index d9e8ccc..24cd7e0 100644 --- a/figure-5-comparative-analysis.ipynb +++ b/figure-5-comparative-analysis.ipynb @@ -81,7 +81,7 @@ "metadata": {}, "outputs": [], "source": [ - "receptors = ['M1', 'M2', 'M3', '5-HT1A', '5-HT2', 'D1'] # interesting receptors\n", + "receptors = ['M1', 'M2', 'M3', '5-HT1A', '5-HT2', 'D1'] # selection of monogenetic receptors\n", "genes=[\n", " siibra.vocabularies.GENE_NAMES.CHRM1,\n", " siibra.vocabularies.GENE_NAMES.CHRM2,\n", @@ -112,6 +112,10 @@ " fcopy = f\n", " fcopy._data_cached = f.data.loc[receptors]\n", " f.plot(ax = axs[j+1, i], **plotargs)\n", + " if modality == siibra.features.molecular.ReceptorDensityFingerprint:\n", + " # add neurotransmitter names to receptor names in xtick labels\n", + " transmitters = [re.sub(r'(^.*\\()|(\\))', '', n) for n in f.neurotransmitters]\n", + " axs[j+1, i].set_xticklabels([f\"{r}\\n({n})\" for r, n in zip(f.receptors, transmitters)])\n", " if ymax[j] is not None:\n", " axs[j+1, i].set_ylim(0, ymax[j])\n", " if 'std' in axs[j+1, i].yaxis.get_label_text():\n", @@ -172,15 +176,6 @@ "### Retrieve cortical patches" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pmap_volume.fetch()" - ] - }, { "cell_type": "code", "execution_count": null, @@ -259,7 +254,7 @@ ], "metadata": { "kernelspec": { - "display_name": "venv", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -273,7 +268,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.15" + "version": "3.10.13" } }, "nbformat": 4,