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{
"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 aniso\n",
"import numpy as np\n",
"import common.lin as lin\n",
"import matplotlib.ticker as ticker"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"def mkViolinPlot(d, ax, ws=0.7):\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(0.005))\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",
" plt.xticks(rotation=90)\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#load FM1 at specified timepoints\n",
"tss, linss = lin.mkSeries1(d=\"../data/FM1/tv/\",\n",
" dExprs=\"../data/geneExpression/\",\n",
" linDataLoc=\"../data/FM1/tracking_data/\",\n",
" ft=lambda t: t in {10, 40, 96, 120, 132})"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Per pattern"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"G = p.mkTGraphN()\n",
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]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"gans = p.calcAnisotropies(regs, tss, linss)\n",
"gans_pat = p.addCombPatterns(gans, tss)\n",
"gans_state = p.getGAnisosPerPattern(G, gans_pat)"
]
},
{
"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'anisotropy rate ($h^{-1}$)')\n",
"ax.yaxis.set_major_locator(ticker.MultipleLocator(0.05))\n",
"\n",
"mkViolinPlot(gans_state, ax)\n",
"\n",
"fout = \"pattern_anisotropy.png\"\n",
"plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
"plt.show()"
]
},
{
"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": "markdown",
"metadata": {},
"source": [
"## Per pattern on graph"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"G = p.mkTGraphN()\n",
"p.addGAnisos(G, gans_pat)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"p.drawTGraph(G, p.ganiso)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Per gene"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"gans_gene = p.getGAnisosPerGene(tss, gans)"
]
},
{
"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'anisotropy ($h^{-1}$)')\n",
"ax.yaxis.set_major_locator(ticker.MultipleLocator(0.05))\n",
"\n",
"mkViolinPlot(gans_gene, ax)\n",
"\n",
"fout = \"gene_anisotropy.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": [
"gans_gene_time = p.getGAnisosPerGeneTime(tss, gans)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"for t in sorted(gans_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'anisotropy ($h^{-1}$)')\n",
" ax.set_ylim((0.0, 0.03))\n",
" ax.yaxis.set_major_locator(ticker.MultipleLocator(0.05))\n",
"\n",
" mkViolinPlot(gans_gene_time[t], ax, ws=0.4)\n",
"\n",
" fout = \"gene_anisotropy_{t}.png\".format(t=t)\n",
" plt.savefig(fout, dpi=300, bbox_inches='tight')\n",
" plt.show()"
]
}
],
"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",