circadian_period_q10.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/dxda6216/q10/blob/main/circadian_period_q10.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Circadian period Q<sub>10</sub> calculator\n",
        "\n",
        "For usage, please take a look at:\n",
        "[https://github.com/dxda6216/q10](https://github.com/dxda6216/q10)\n"
      ],
      "metadata": {
        "id": "5DWMWfNrVHi-"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "### This is a simple script to calculate Q10 values for circadian period\n",
        "### length by using SciPy Optimize non-linear least squares fit on Colab.\n",
        "### Copyright (c) 2022 by dxda6216 (dxda6216 AT gmail DOT com)\n",
        "###\n",
        "#@title Q10 calculator\n",
        "import numpy as np\n",
        "from scipy.optimize import curve_fit\n",
        "from matplotlib import pyplot as plt\n",
        "\n",
        "#@markdown Input data, then hit **Runtime** -> **Run all** (or press **Ctrl+F9**).\n",
        "# Data description (plot title)\n",
        "Data_description = \"Compound XYZ\" #@param {type:\"string\"}\n",
        "\n",
        "# Temperature data\n",
        "Temperatures = 33.4, 33.4, 34.3, 34.3, 35.2, 35.2, 35.8, 35.8, 36.3, 36.3, 36.9, 36.9, 37.8, 37.8, 38.6, 33.4, 33.4, 34.3, 34.3, 35.2, 35.2, 35.8, 35.8, 36.3, 36.3, 36.9, 36.9, 37.8, 37.8, 38.6, 38.6, 39.1, 39.1, 40.4, 40.4 #@param {type:\"raw\"}\n",
        "x = np.array(Temperatures)\n",
        "\n",
        "# Period data\n",
        "Periods =  37.070, 38.060, 37.780, 35.200, 32.840, 33.980, 33.610, 32.750, 32.430, 31.950, 35.000, 31.920, 35.800, 30.710, 30.690, 37.470, 37.460, 35.100, 35.770, 33.910, 34.160, 32.730, 33.350, 33.120, 32.950, 34.290, 32.130, 33.110, 30.550, 26.450, 31.720, 33.430, 28.520, 31.100, 27.360 #@param {type:\"raw\"}\n",
        "y = np.array(Periods)\n",
        "\n",
        "# Printing the data\n",
        "print('Temperature = ', x)\n",
        "print('Period = ', y, '\\n')\n",
        "\n",
        "# Figure Settings ON of OFF\n",
        "Set_graphical_parameters_of_figure = \"No (Graph axes, tick marks, etc will automatically be adjusted)\" #@param [\"No (Graph axes, tick marks, etc will automatically be adjusted)\", \"Yes (Set the parameters)\"]\n",
        "\n",
        "# Figure graphical_parameter settings\n",
        "# psx[0] : figure size - width\n",
        "# psx[1] : figure size - height\n",
        "# psx[2] : X-axis scale - min\n",
        "# psx[3] : X-axis scale - max\n",
        "# psx[4] : X-axis ticks - starting\n",
        "# psx[5] : X-axis ticks - ending\n",
        "# psx[6] : X-axis ticks - interval\n",
        "# psx[7] : Y-axis scale - min\n",
        "# psx[8] : Y-axis scale - max\n",
        "# psx[9] : Y-axis ticks - starting\n",
        "# psx[10] : Y-axis ticks - ending\n",
        "# psx[11] : Y-axis ticks - interval\n",
        "# psx[12] : Fitted curve - starting\n",
        "# psx[13] : Fitted curve - ending\n",
        "Figure_graphical_parameters =  8, 6, 27, 45, 28, 45, 2, 14, 45, 14, 45, 2, 28, 43 #@param {type:\"raw\"}\n",
        "psx = np.array(Figure_graphical_parameters)\n",
        "\n",
        "# Displaying Tab-delimited data Yes or No\n",
        "Display_tab_delimited_data = \"No\" #@param [\"No\", \"Yes\"]\n",
        "\n",
        "# Defining an equation for curve fitting\n",
        "# fitting parameters:\n",
        "#     tau37 : period at 37 degree Celsius\n",
        "#     q10 : temperature coefficient (Q10)\n",
        "def func(x, tau37, q10):\n",
        "\treturn tau37 / ( q10 ** ( ( x - 37 ) * 0.1 ) )\n",
        "\n",
        "# Initial values for the fitting parameters\n",
        "p0 = np.array([24.000, 1.000])\n",
        "\n",
        "# Fitting the data to the defined equation\n",
        "popt, pcov = curve_fit(func, x, y, p0)\n",
        "\n",
        "residuals = y - func(x, *popt)\n",
        "ss_residuals = np.sum(residuals**2)\n",
        "ss_total = np.sum((y-np.mean(y))**2)\n",
        "r_squared = 1 - ( ss_residuals / ss_total )\n",
        "\n",
        "# Printing the results\n",
        "print(u'Tau37 (estimated period length at 37\\u00B0C) =', '{:.3f}'.format(popt[0]), u'\\u00B1', '{:.3f}'.format(pcov[0,0]**0.5))\n",
        "print(u'Q10 (temperature coefficient) =', '{:.3f}'.format(popt[1]), u'\\u00B1', '{:.3f}'.format(pcov[1,1]**0.5))\n",
        "print(u'R\\u00B2 =', '{:.6f}'.format(r_squared), u'\\n')\n",
        "\n",
        "\n",
        "# Plotting data and fitted curve\n",
        "if Set_graphical_parameters_of_figure == \"Yes (Set the parameters)\":\n",
        "\tfig = plt.figure(figsize = (psx[0],psx[1]))\n",
        "\tfcx = np.linspace(psx[12], psx[13], 200)\n",
        "\tif psx[4] < psx[2]:\n",
        "\t\tpsx[4] = psx[2]\n",
        "\tif psx[5] >= psx[3]:\n",
        "\t\tpsx[5] = psx[3] + 1\n",
        "\tif psx[9] < psx[7]:\n",
        "\t\tpsx[9] = psx[7]\n",
        "\tif psx[10] >= psx[8]:\n",
        "\t\tpsx[10] = psx[8] + 1\n",
        "\tplt.xlim(psx[2], psx[3])\n",
        "\tplt.ylim(psx[7], psx[8])\n",
        "\tplt.xticks(np.arange(psx[4], psx[5], psx[6]))\n",
        "\tplt.yticks(np.arange(psx[9], psx[10], psx[11]))\n",
        "else:\n",
        "\tfig = plt.figure(figsize = (8,6))\n",
        "\tfcxmin = int( min(x) - ( max(x) - min(x) ) * 0.250 )\n",
        "\tfcxmax = int( max(x) + ( max(x) - min(x) ) * 0.250 ) + 1\n",
        "\tfcx = np.linspace(fcxmin, fcxmax, 200)\n",
        "\n",
        "plt.plot(x, y, 'o', color ='red', label ='data')\n",
        "fcy = func(fcx, popt[0], popt[1])\n",
        "plt.plot(fcx, fcy, '--', color='blue', label ='fit  tau37=%5.3f, Q10=%5.3f' % tuple(popt))\n",
        "plt.title(Data_description)\n",
        "plt.xlabel(u'Temperature (\\u00B0C)')\n",
        "plt.ylabel('Period (hours)')\n",
        "\n",
        "#if Display_tab_delimited_data == \"Yes\":\n",
        "#\tprint(u'Dataset')\n",
        "#\tprint (u'Temp (\\u00B0C)\\tPeriod (hours)')\n",
        "#\tycount = 0\n",
        "#\tfor xseq in x:\n",
        "#\t\tprint(str(xseq)+'\\t'+str(y[ycount]))\n",
        "#\t\tycount += 1\n",
        "#\tprint(u'\\nFitted Curve')\n",
        "#\tprint (u'Temp (\\u00B0C)\\tPeriod (hours)')\n",
        "#\tfcycount = 0\n",
        "#\tfor fcxseq in fcx:\n",
        "#\t\tprint('{:.3f}'.format(fcxseq)+'\\t'+'{:.3f}'.format(fcy[fcycount]))\n",
        "#\t\tfcycount += 1\n",
        "#\tprint(u'\\n')\n",
        "\n",
        "if Display_tab_delimited_data == \"Yes\":\n",
        "\tfix = np.array(range(100, 501, 1))\n",
        "\tflx = fix / 10\n",
        "\tfly = func(flx, popt[0], popt[1])\n",
        "\tprint(u'Dataset')\n",
        "\tprint (u'Temp (\\u00B0C)\\tPeriod (hours)')\n",
        "\tycount = 0\n",
        "\tfor xseq in x:\n",
        "\t\tprint(str(xseq)+'\\t'+str(y[ycount]))\n",
        "\t\tycount += 1\n",
        "\tprint(u'\\nFitted Curve')\n",
        "\tprint (u'Temp (\\u00B0C)\\tPeriod (hours)')\n",
        "\tfcycount = 0\n",
        "\tfor flxseq in flx:\n",
        "\t\tprint('{:.1f}'.format(flx[fcycount])+'\\t'+'{:.3f}'.format(fly[fcycount]))\n",
        "\t\tfcycount += 1\n",
        "\tprint(u'\\n')\n",
        "\n",
        "plt.legend()\n",
        "plt.show()\n",
        "\n",
        "### End of script"
      ],
      "metadata": {
        "id": "NI2hnwFuVc1z",
        "cellView": "form"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}