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mhenault1 · Oct 13, 2022 · 4218846 · 4218846
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Showing 5 changed files with 439 additions and 1,203 deletions.
diff --git a/assembly_comparison.ipynb b/assembly_comparison.ipynb
@@ -141,9 +141,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = plt.figure(figsize=[10,10])\n",
+    "fig = plt.figure(figsize=[8,8])\n",
     "gs = plt.GridSpec(ncols=2, nrows=2, left=0.15, right=0.96, bottom=0.15, top=0.94,\n",
-    "                  hspace=0.6, wspace=0.5)\n",
+    "                  hspace=0.6, wspace=0.6)\n",
     "m_alias = {'snp_count':'single nucleotide variants',\n",
     "           'indel_count': 'single nucleotide indels',\n",
     "           'gap_count':'gaps',\n",
@@ -158,9 +158,9 @@
     "        sns.heatmap(df, ax=ax, cmap='bwr', center=0, annot=True, fmt='.0f', cbar=False)\n",
     "    else:\n",
     "        sns.heatmap(df, ax=ax, cmap='Blues', annot=True, fmt='.0f', cbar=False)\n",
-    "    ax.set_yticklabels(assemblies['nanopore'].apply(lambda x: assemblies_alias[x]))\n",
+    "    ax.set_yticklabels(assemblies['nanopore'].apply(lambda x: assemblies_alias[x]), rotation=45, va='top')\n",
     "    ax.set_ylabel('')\n",
-    "    ax.set_xticklabels(assemblies['atp6'].apply(lambda x: assemblies_alias[x]))\n",
+    "    ax.set_xticklabels(assemblies['atp6'].apply(lambda x: assemblies_alias[x]), rotation=45, ha='right')\n",
     "    ax.set_xlabel('')\n",
     "    ax.set_title(m_alias[m], size=14)\n",
     "    \n",
@@ -170,7 +170,7 @@
     "fig.text(0.52, 0.47, 'D', size=24, weight='bold')\n",
     "    \n",
     "#plt.show()\n",
-    "#plt.savefig('/home/mathieu/mhenault_landrylab/Publications/mito_ma/resubmission_GRes/fig/assembly_comparison.svg')\n",
+    "#plt.savefig('/home/mathieu/mhenault_landrylab/Publications/mito_ma/resubmission2_GRes/fig/assembly_comparison.svg')\n",
     "plt.close()"
    ]
   }

diff --git a/divergence.ipynb b/divergence.ipynb
@@ -277,7 +277,7 @@
    "id": "8c3970f9-f0cf-4f95-9965-5bd26ad2bcb6",
    "metadata": {},
    "source": [
-    "# Fig S15"
+    "# Fig S4"
    ]
   },
   {
@@ -287,25 +287,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, axes = plt.subplots(ncols=2, figsize=[8,4], \n",
-    "                         gridspec_kw=dict(wspace=0.7, width_ratios=[3,2], left=0.12, right=0.98, top=0.9, bottom=0.15))\n",
+    "fig, axes = plt.subplots(nrows=2, figsize=[3,6], \n",
+    "                         gridspec_kw=dict(hspace=0.4, height_ratios=[3,2], left=0.28, right=0.93, top=0.82, bottom=0.12))\n",
     "ax = axes[0]\n",
     "sns.scatterplot(x='nuc_dist', y='mt_dist', hue='cross', palette=cross_color, data=dist_per_cross, ax=ax)\n",
     "ax.set_xlabel('nuc divergence (subs site$^{-1}$)')\n",
-    "ax.set_ylabel('mt divergence (subs site$^{-1}$)')\n",
-    "ax.legend(loc=6, bbox_to_anchor=[1,0.5], frameon=False)\n",
+    "ax.set_ylabel('mt divergence\\n(subs site$^{-1}$)')\n",
+    "ax.legend(loc=6, bbox_to_anchor=[-0.05,1.25], ncol=3, frameon=False, handlelength=0.3)\n",
     "\n",
     "ax = axes[1]\n",
     "ax.bar(dist_per_cross['cross'], dist_per_cross['ratio'], color=[cross_color[cross] for cross in cross_order],  width=0.5)\n",
     "ax.set_xlabel('')\n",
     "ax.set_xticklabels(cross_order, rotation=90)\n",
-    "ax.set_ylabel('divergence ratio (nuc/mt)')\n",
+    "ax.set_ylabel('divergence ratio\\n(nuc/mt)')\n",
     "\n",
-    "fig.text(0.03, 0.93, 'C', weight='bold', size=24)\n",
-    "fig.text(0.63, 0.93, 'D', weight='bold', size=24)\n",
+    "fig.text(0.01, 0.93, 'C', weight='bold', size=24)\n",
+    "fig.text(0.01, 0.35, 'D', weight='bold', size=24)\n",
     "\n",
     "sns.despine()\n",
-    "#plt.savefig('/home/mathieu/mhenault_landrylab/Publications/mito_ma/resubmission_GRes/fig/mito_nuc_divergence_CD.svg')\n",
+    "#plt.savefig('/home/mathieu/mhenault_landrylab/Publications/mito_ma/resubmission2_GRes/fig/mito_nuc_divergence_CD.svg')\n",
     "#plt.show()\n",
     "plt.close()"
    ]