diff --git a/notebooks/l1_morph_metrics.ipynb b/notebooks/l1_morph_metrics.ipynb index 19a2e52..5950448 100755 --- a/notebooks/l1_morph_metrics.ipynb +++ b/notebooks/l1_morph_metrics.ipynb @@ -51,7 +51,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -76,7 +76,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -128,7 +128,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -144,7 +144,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -155,7 +155,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -165,7 +165,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -183,7 +183,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -194,6 +194,102 @@ "combined = pd.concat([mouse_l12, human_l12], sort=False)" ] }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/local1/storage/envs/ipfx3/lib/python3.7/site-packages/statsmodels/base/model.py:1873: ValueWarning: covariance of constraints does not have full rank. The number of constraints is 9, but rank is 8\n", + " 'rank is %d' % (J, J_), ValueWarning)\n", + "/local1/storage/envs/ipfx3/lib/python3.7/site-packages/statsmodels/base/model.py:1873: ValueWarning: covariance of constraints does not have full rank. The number of constraints is 9, but rank is 8\n", + " 'rank is %d' % (J, J_), ValueWarning)\n" + ] + }, + { + "data": { + "text/html": [ + "
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eta_p_speciespval_speciespval_species:homology_typersquaredinteraction
feature
dendrite_cross_section_peak0.1485630.0000980.4472070.228495False
dendrite_volume0.0202630.1474590.4472070.157628False
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" + ], + "text/plain": [ + " eta_p_species pval_species \\\n", + "feature \n", + "dendrite_cross_section_peak 0.148563 0.000098 \n", + "dendrite_volume 0.020263 0.147459 \n", + "\n", + " pval_species:homology_type rsquared interaction \n", + "feature \n", + "dendrite_cross_section_peak 0.447207 0.228495 False \n", + "dendrite_volume 0.447207 0.157628 False " + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "groups = ['PAX6', 'LAMP5', 'MC4R', 'L1 VIP']\n", + "features = ['dendrite_volume', 'dendrite_cross_section_peak']\n", + "res = utils.run_species_subclass_stats(combined, features, groups=groups)\n", + "res" + ] + }, { "cell_type": "code", "execution_count": 13,