diff --git a/growthAnalysis/grates.ipynb b/growthAnalysis/grates.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..07277ebe801f4b1b72b2c5acaa8b7964075508e2
--- /dev/null
+++ b/growthAnalysis/grates.ipynb
@@ -0,0 +1,478 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import patternTransitions as p\n",
+ "from itertools import repeat\n",
+ "import seaborn as sns\n",
+ "import matplotlib.pyplot as plt\n",
+ "from mpl_toolkits.mplot3d import Axes3D\n",
+ "import common.seg as seg\n",
+ "import _pickle as cPickle\n",
+ "import common.lin as lin\n",
+ "import aniso\n",
+ "import numpy as np\n",
+ "import matplotlib.ticker as ticker"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from os.path import join"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plot_params = {'01' : {'elev': 120, 'azim' : 270, 'vmax':0.4},\n",
+ " '02' : {'elev': 70, 'azim' : -20, 'vmax':0.3},\n",
+ " '03' : {'elev': 90, 'azim' : 270, 'vmax':0.2},\n",
+ " '04' : {'elev':80, 'azim': 50, 'vmax': 0.2},\n",
+ " '05' : {'elev':70, 'azim': 220, 'vmax':0.2},\n",
+ " '06' : {'elev':90, 'azim': 270, 'vmax':0.2}}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "#fid='01'\n",
+ "\n",
+ "#tssFn = join(dataDir, \"lins_allflowers/f{fid}_tss.pkl\".format(fid=fid))\n",
+ "#linssFn = join(dataDir, \"lins_allflowers/f{fid}_linss.pkl\".format(fid=fid))\n",
+ "\n",
+ "#with open(tssFn, 'rb') as tssF:\n",
+ "# tss = cPickle.load(tssF, encoding='latin1')\n",
+ "\n",
+ "#with open(linssFn, 'rb') as linssF:\n",
+ "# linss = cPickle.load(linssF, encoding='latin1')\n",
+ "\n",
+ "#if fid=='01':\n",
+ "# lin.filterL1(tss)\n",
+ "#else:\n",
+ "# tss = dict([(t, seg.filterL1(ts)) for t, ts in tss.items()])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "dataDir = \"../data/\"\n",
+ "tss, linss = lin.mkSeries1(dataDir)\n",
+ "lin.filterL1(tss)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def mkViolinPlot(d, ax, ws=0.7, vert=False):\n",
+ " xs_labs = sorted(d.keys())\n",
+ " xs = range(len(xs_labs))\n",
+ " ys = [d[x] for x in xs_labs]\n",
+ " \n",
+ " #ax.yaxis.set_major_locator(ticker.MultipleLocator(0.05))\n",
+ " sns.set_style(\"whitegrid\", {'grid.linestyle':'--'})\n",
+ " cls = sns.color_palette()\n",
+ " ax.set_xticks(xs)\n",
+ " ax.set_xticklabels(xs_labs)\n",
+ " violin_parts = ax.violinplot(ys, xs, showmeans=True, widths=ws)\n",
+ " for pc in violin_parts['bodies']:\n",
+ " pc.set_facecolor(\"#f5d742\")\n",
+ " pc.set_edgecolor('black')\n",
+ "\n",
+ " for partname in ('cbars','cmins','cmaxes','cmeans'):\n",
+ " vp = violin_parts[partname]\n",
+ " vp.set_edgecolor('red')\n",
+ " vp.set_linewidth(0.5)\n",
+ " \n",
+ " if vert:\n",
+ " plt.xticks(rotation=90)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Per pattern"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import grates as grs\n",
+ "\n",
+ "G = p.mkTGraphN()\n",
+ "grates = grs.grates_avg_cons(tss, linss)\n",
+ "grates_pats = p.addCombPatterns(grates, tss)\n",
+ "\n",
+ "grs_state = p.getGAnisosPerPattern(G, grates_pats)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plt.rcParams.update({'font.size': 12})\n",
+ "fig = plt.figure(figsize=(9, 4.5))\n",
+ "ax = fig.add_subplot('111')\n",
+ "\n",
+ "ax.set_xlabel(\"cell state\")\n",
+ "ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
+ "ax.set_ylim((-0.05, 0.15))\n",
+ "ax.yaxis.set_ticks(np.arange(-0.05, 0.15, 0.1))\n",
+ "ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
+ "\n",
+ "mkViolinPlot(grs_state, ax)\n",
+ "\n",
+ "fout = \"state_growth_rates.png\"\n",
+ "plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
+ "plt.show()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Per pattern on graph"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "p.addGRates(G, grates_pats) "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "p.drawTGraph(G, p.gr)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Per gene"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "grates_gene = p.getGAnisosPerGene(tss, grates)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fig = plt.figure(figsize=(10, 5))\n",
+ "ax = fig.add_subplot('111')\n",
+ "\n",
+ "ax.set_xlabel(\"gene\")\n",
+ "ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
+ "ax.set_ylim((-0.05, 0.15))\n",
+ "ax.yaxis.set_ticks(np.arange(-0.05, 0.15, 0.1))\n",
+ "ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
+ "\n",
+ "mkViolinPlot(grates_gene, ax, vert=True)\n",
+ "\n",
+ "fout = \"gene_grates.png\"\n",
+ "plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
+ "plt.show()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Per gene, per stage"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def tToStage(t):\n",
+ " if t==10: return 0\n",
+ " elif t==40: return 1\n",
+ " elif t==96: return 2\n",
+ " elif t==120: return 3\n",
+ " elif t==132: return 4"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "grates_gene_time = p.getGAnisosPerGeneTime(tss, grates)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "for t in sorted(grates_gene_time.keys()):\n",
+ " fig = plt.figure(figsize=(10, 5))\n",
+ " ax = fig.add_subplot('111')\n",
+ " \n",
+ " ax.set_title(\"stage {t}\".format(t=tToStage(t)))\n",
+ " ax.set_xlabel(\"gene\")\n",
+ " ax.set_ylabel(r'growth rate ($h^{-1}$)')\n",
+ " ax.set_ylim((-0.05, 0.15))\n",
+ " ax.yaxis.set_major_locator(ticker.MultipleLocator(0.1))\n",
+ "\n",
+ " mkViolinPlot(grates_gene_time[t], ax, ws=0.4, vert=True)\n",
+ "\n",
+ " fout = \"gene_growth_{t}.png\".format(t=t)\n",
+ " plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
+ " plt.show()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Growth rate distributions (all to all timepoints)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import grates as grs\n",
+ "timepoints = sorted(tss.keys())\n",
+ "n = len(timepoints)\n",
+ "\n",
+ "fig = plt.figure(figsize=(10, 8))\n",
+ "plt.subplots_adjust(hspace=0.85, wspace=0.5)\n",
+ "\n",
+ "for i, t1 in enumerate(timepoints):\n",
+ " for k, t2 in enumerate(timepoints):\n",
+ " print(t1, end=\",\")\n",
+ " print(t2, end=\" \")\n",
+ " if t1 > t2:\n",
+ " ax = plt.subplot2grid((n, n), (i, k))\n",
+ " #plot forward\n",
+ " plt.rcParams.update({'font.size': 8})\n",
+ " ax.set_title(str(t2) + \"h\" + \"-\" + str(t1)+\"h\")\n",
+ " plt.rcParams.update({'font.size': 10})\n",
+ " ax.set_xlim([-0.05, 0.15])\n",
+ " ax.set_xticks([0.0, 0.05, 0.1])\n",
+ " ans = grs.grates_forward(tss, linss, t2, t1)\n",
+ " ans_ = np.array([an for _, an in ans.items() if an])\n",
+ " sns.distplot(ans_, ax=ax) "
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Growth rate distributions (all to all timepoints) on templates"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import grates as grs"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fid = '01'\n",
+ "timepoints = sorted(tss.keys())[::]\n",
+ "n = len(timepoints)\n",
+ "plt.rcParams.update({'font.size': 8})\n",
+ "def plot_ans(ts, ans, ax, s=10, vmax=1.0):\n",
+ " xs = [c.pos.x for c in ts]\n",
+ " ys = [c.pos.y for c in ts]\n",
+ " zs = [c.pos.z for c in ts]\n",
+ " cs = [ans.get(c.cid, 0.0) for c in ts]\n",
+ " \n",
+ " \n",
+ " points = ax.scatter(xs, ys, zs, c=cs, cmap=plt.cm.jet, alpha=0.9, s=s, vmin=0.0, vmax=vmax,\n",
+ " edgecolors='black', linewidths=0.5)\n",
+ " plt.colorbar(points, shrink=0.5, ticks=[0.0, vmax])\n",
+ " plt.axis('off')\n",
+ " \n",
+ " return\n",
+ "\n",
+ "fig = plt.figure(figsize=(9, 5))\n",
+ "\n",
+ "for i, t1 in enumerate(timepoints):\n",
+ " for k, t2 in enumerate(timepoints):\n",
+ " print(t1, t2, end=\" \")\n",
+ " if t1 < t2:\n",
+ " ax = plt.subplot2grid((n, n), (i, k), projection='3d')\n",
+ " ax.set_title(str(t1)+\"h\" + \"-\" + str(t2) + \"h\")\n",
+ " ax.view_init(elev=plot_params[fid]['elev'], azim=plot_params[fid]['azim'])\n",
+ " #plot\n",
+ " ans = grs.grates_forward(tss, linss, t1, t2)\n",
+ " ans_ = dict([(cid, an) for cid, an in ans.items() if an])\n",
+ " plot_ans(tss[t1], ans_, ax, vmax=0.15)\n",
+ " elif t1 > t2:\n",
+ " ax = plt.subplot2grid((n, n), (i, k), projection='3d')\n",
+ " ax.set_title(str(t2)+\"h\" + \"-\" + str(t1) + \"h\")\n",
+ " ax.view_init(elev=plot_params[fid]['elev'], azim=plot_params[fid]['azim'])\n",
+ " #plot\n",
+ " ans = grs.grates_backward(tss, linss, t2, t1)\n",
+ " ans_ = dict([(cid, an) for cid, an in ans.items() if an])\n",
+ " plot_ans(tss[t1], ans_, ax, vmax=0.15)\n",
+ " else:\n",
+ " ax = plt.subplot2grid((n, n), (i, k))\n",
+ " ax.set_xlim(0.0, 1.0)\n",
+ " ax.set_ylim(0.0, 1.0)\n",
+ " ax.text(0.4, 0.5, str(t1)+\"h\", transform = ax.transAxes, fontsize=11)\n",
+ " ax.axis('off')\n",
+ " \n",
+ "fout = \"gratesTs_f{fid}.png\".format(fid=fid)\n",
+ "plt.savefig(fout, dpi=300, bbox_inches='tight')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## All to last"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import grates as grs"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def tToStage(t):\n",
+ " if t==10: return 0\n",
+ " elif t==40: return 1\n",
+ " elif t==96: return 2\n",
+ " elif t==120: return 3\n",
+ " elif t==132: return 4"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "timepoints = sorted(tss.keys())\n",
+ "n = len(timepoints)\n",
+ "plt.rcParams.update({'font.size': 8})\n",
+ "\n",
+ "def plot_ans(ts, ans, ax, s=10, vmax=1.0):\n",
+ " xs = [c.pos.x for c in ts]\n",
+ " ys = [c.pos.y for c in ts]\n",
+ " zs = [c.pos.z for c in ts]\n",
+ " cs = [ans.get(c.cid, 0.0) for c in ts]\n",
+ " \n",
+ " \n",
+ " points = ax.scatter(xs, ys, zs, c=cs, cmap=plt.cm.jet, alpha=0.9, s=s, vmin=0.0, vmax=vmax,\n",
+ " edgecolors='black', linewidths=0.5)\n",
+ " plt.colorbar(points, shrink=0.5, ticks=[0.0, vmax])\n",
+ " plt.axis('off')\n",
+ " \n",
+ " return\n",
+ "\n",
+ "fig = plt.figure(figsize=(6, 2.25))\n",
+ "\n",
+ "t2 = timepoints[-1]\n",
+ "for i, t1 in enumerate(timepoints[:-1]):\n",
+ " ax = plt.subplot2grid((2, n), (0, i), projection='3d')\n",
+ " ax.set_title(\"{s1} -> ({s2})\".format(s1=tToStage(t1), s2 = tToStage(t2)))\n",
+ " ax.view_init(elev=plot_params[fid]['elev'], azim=plot_params[fid]['azim'])\n",
+ " #plot\n",
+ " ans = grs.grates_forward(tss, linss, t1, t2)\n",
+ " ans_ = dict([(cid, an) for cid, an in ans.items() if an])\n",
+ " plot_ans(tss[t1], ans_, ax, vmax=0.15)\n",
+ " \n",
+ " ax = plt.subplot2grid((2, n), (1, i), projection='3d')\n",
+ " ax.set_title(\"({s1}) -> {s2}\".format(s1=tToStage(t1), s2 = tToStage(t2)))\n",
+ " ax.view_init(elev=plot_params[fid]['elev'], azim=plot_params[fid]['azim'])\n",
+ " #plot\n",
+ " ans = grs.grates_backward(tss, linss, t1, t2)\n",
+ " ans_ = dict([(cid, an) for cid, an in ans.items() if an])\n",
+ " plot_ans(tss[t2], ans_, ax, vmax=0.15)\n",
+ " \n",
+ "plt.savefig(\"presentation_figures/grates_tolast\", dpi=300, bbox_inches = 'tight') "
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}