Merge pull request #155 from markovmodel/revision-cw

Revision cw

Author: cwehmeyer

manuscript/figures/figure_2.pdf

@@ -1221,7 +1221,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This is now the first figure which sketches the entire estimation and validation part:"
+    "This is Figure 2 (a,b,c,d) which sketches the system and coordinates part:"
    ]
   },
   {
@@ -1230,20 +1230,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = plt.figure(figsize=(3.47, 6.77))\n",
+    "fig = plt.figure(figsize=(3.47, 4.65))\n",
     "gw = int(np.floor(0.5 + 1000 * fig.get_figwidth()))\n",
     "gh = int(np.floor(0.5 + 1000 * fig.get_figheight()))\n",
     "gs = plt.GridSpec(gh, gw)\n",
     "gs.update(hspace=0.0, wspace=0.0, left=0.0, right=1.0, bottom=0.0, top=1.0)\n",
     "\n",
     "ax_box = fig.add_subplot(gs[:, :])\n",
     "ax_box.set_axis_off()\n",
-    "ax_box.text(0.00, 0.98, '(a)', size=10, zorder=1)\n",
-    "ax_box.text(0.00, 0.71, '(b)', size=10)\n",
-    "ax_box.text(0.55, 0.71, '(c)', size=10)\n",
-    "ax_box.text(0.00, 0.46, '(d)', size=10)\n",
-    "ax_box.text(0.00, 0.32, '(e)', size=10)\n",
-    "ax_box.text(0.00, 0.14, '(f)', size=10)\n",
+    "ax_box.text(0.00, 0.95, '(a)', size=10, zorder=1)\n",
+    "ax_box.text(0.00, 0.58, '(b)', size=10)\n",
+    "ax_box.text(0.55, 0.58, '(c)', size=10)\n",
+    "ax_box.text(0.00, 0.22, '(d)', size=10)\n",
     "\n",
     "ax_mol = fig.add_subplot(gs[:1600, -2820:-400])\n",
     "ax_mol.set_axis_off()\n",
@@ -1294,20 +1292,48 @@
     "ax_tic2.set_ylabel('IC 2')\n",
     "ax_tic2.set_xlabel('time / ns')\n",
     "\n",
-    "ax_its = fig.add_subplot(gs[4680:5480, 400:3350])\n",
+    "fig.savefig('data/figure_2.pdf', dpi=300)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Next is Figure 3 (a,b) which shows estimation and validation:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig = plt.figure(figsize=(3.47, 2.60))\n",
+    "gw = int(np.floor(0.5 + 1000 * fig.get_figwidth()))\n",
+    "gh = int(np.floor(0.5 + 1000 * fig.get_figheight()))\n",
+    "gs = plt.GridSpec(gh, gw)\n",
+    "gs.update(hspace=0.0, wspace=0.0, left=0.0, right=1.0, bottom=0.0, top=1.0)\n",
+    "\n",
+    "ax_box = fig.add_subplot(gs[:, :])\n",
+    "ax_box.set_axis_off()\n",
+    "ax_box.text(0.00, 0.95, '(a)', size=10)\n",
+    "ax_box.text(0.00, 0.36, '(b)', size=10)\n",
+    "\n",
+    "ax_its = fig.add_subplot(gs[50:1300, 400:3350])\n",
     "pyemma.plots.plot_implied_timescales(its, units='ns', dt=0.1, ax=ax_its, nits=4, ylog=True)\n",
     "ax_its.set_ylim(1, ax_its.get_ylim()[1])\n",
     "ax_its.set_xlabel(r'lag time $\\tau$ / ns')\n",
     "\n",
     "ax_ck = [\n",
-    "    fig.add_subplot(gs[5940:6510, 400:970]),\n",
-    "    fig.add_subplot(gs[5940:6510, 995:1565]),\n",
-    "    fig.add_subplot(gs[5940:6510, 1590:2160]),\n",
-    "    fig.add_subplot(gs[5940:6510, 2185:2755]),\n",
-    "    fig.add_subplot(gs[5940:6510, 2780:3350])]\n",
+    "    fig.add_subplot(gs[1730:2300, 400:970]),\n",
+    "    fig.add_subplot(gs[1730:2300, 995:1565]),\n",
+    "    fig.add_subplot(gs[1730:2300, 1590:2160]),\n",
+    "    fig.add_subplot(gs[1730:2300, 2185:2755]),\n",
+    "    fig.add_subplot(gs[1730:2300, 2780:3350])]\n",
     "\n",
     "for k, ax in enumerate(ax_ck):\n",
-    "    lest, lpred = _add_ck_subplot(cktest, ax, k, k, ipos=cktest.nsets - 1, dt=0.1, units='ns')\n",
+    "    lest, lpred = _add_ck_subplot(\n",
+    "        cktest, ax, k, k, ipos=cktest.nsets - 1, dt=0.1, units='ns', linewidth=0.7)\n",
     "    if k > 0:\n",
     "        ax.set_yticks([])\n",
     "predlabel = 'predict ({:3.1f}%)'.format(100.0 * cktest.conf)\n",
@@ -1319,14 +1345,14 @@
     "    loc='upper left',\n",
     "    bbox_to_anchor=(-0.4, 1.45))\n",
     "\n",
-    "fig.savefig('data/figure_2.pdf', dpi=300)"
+    "fig.savefig('data/figure_3.pdf', dpi=300)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "And this is the second figure which highlights the analysis part:"
+    "Figure 4 (a,b,c,d) highlights the basic analysis part using map plots:"
    ]
   },
   {
@@ -1418,7 +1444,14 @@
     "ax_flux.set_xlabel('IC 1')\n",
     "ax_flux.set_yticklabels([])\n",
     "\n",
-    "fig.savefig('data/figure_3.pdf', dpi=300)"
+    "fig.savefig('data/figure_4.pdf', dpi=300)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Figure 5 visualizes the $\\mathcal{S}_2\\to\\mathcal{S}_4$ committor:"
    ]
   },
   {
@@ -1464,7 +1497,14 @@
     "    show_committor=True)\n",
     "flux_ax.set_xticks(np.arange(0, 1.2, .2))\n",
     "\n",
-    "fig.savefig('data/figure_4.pdf', dpi=300)"
+    "fig.savefig('data/figure_5.pdf', dpi=300)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And, finally, Figure 6 (a,b) depicts the Trp-1 autocorrelation:"
    ]
   },
   {
@@ -1523,7 +1563,7 @@
     "ax_rlx.set_xlim((eq_time_ml[1], eq_time_ml[-1]))\n",
     "ax_rlx.set_xlabel(r'time / ns')\n",
     "\n",
-    "fig.savefig('data/figure_5.pdf', dpi=300)"
+    "fig.savefig('data/figure_6.pdf', dpi=300)"
    ]
   },
   {