Made a notebook to extract SeqFISH count matrices

Analysis/SeqFISH/Extract SeqFISH count matrices.ipynb

@@ -0,0 +1,169 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Populating the interactive namespace from numpy and matplotlib\n"
+     ]
+    }
+   ],
+   "source": [
+    "%pylab inline\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "exp_mat = pd.read_excel('mmc6.xlsx', 0, header=None, index_col=0)\n",
+    "\n",
+    "field_vector = pd.read_excel('mmc6.xlsx', 1, header=None).T\n",
+    "field_vector.index += 1\n",
+    "field_vector.columns = ['field']\n",
+    "\n",
+    "sample_info = pd.read_excel('mmc6.xlsx', 2, header=None)\n",
+    "sample_info.index += 1\n",
+    "sample_info.columns = ['x', 'y', 'z']\n",
+    "\n",
+    "sample_info = sample_info.join(field_vector)\n",
+    "\n",
+    "sample_info['total_count'] = exp_mat.sum(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(249, 3585)"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "exp_mat.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!mkdir -p individual_fields"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for field, field_si in sample_info.groupby('field'):\n",
+    "    field_si.to_csv(f'individual_fields/field_{field}_sample_info.csv')\n",
+    "    exp_mat.T.loc[field_si.index].to_csv(f'individual_fields/field_{field}_counts.csv')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "field_33_counts.csv       field_40_counts.csv       field_47_counts.csv\r\n",
+      "field_33_sample_info.csv  field_40_sample_info.csv  field_47_sample_info.csv\r\n",
+      "field_34_counts.csv       field_41_counts.csv       field_48_counts.csv\r\n",
+      "field_34_sample_info.csv  field_41_sample_info.csv  field_48_sample_info.csv\r\n",
+      "field_35_counts.csv       field_42_counts.csv       field_49_counts.csv\r\n",
+      "field_35_sample_info.csv  field_42_sample_info.csv  field_49_sample_info.csv\r\n",
+      "field_36_counts.csv       field_43_counts.csv       field_50_counts.csv\r\n",
+      "field_36_sample_info.csv  field_43_sample_info.csv  field_50_sample_info.csv\r\n",
+      "field_37_counts.csv       field_44_counts.csv       field_51_counts.csv\r\n",
+      "field_37_sample_info.csv  field_44_sample_info.csv  field_51_sample_info.csv\r\n",
+      "field_38_counts.csv       field_45_counts.csv       field_52_counts.csv\r\n",
+      "field_38_sample_info.csv  field_45_sample_info.csv  field_52_sample_info.csv\r\n",
+      "field_39_counts.csv       field_46_counts.csv       field_53_counts.csv\r\n",
+      "field_39_sample_info.csv  field_46_sample_info.csv  field_53_sample_info.csv\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "ls individual_fields/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.6.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

Analysis/SeqFISH/SeqFISH Analysis.ipynb

@@ -1401,7 +1401,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.0"
+   "version": "3.6.3"
   }
  },
  "nbformat": 4,