{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Meta-Niche" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "> This was used as the second part of co-localization estimation in our paper. For detailed information, see [tutorial](https://github.com/BGI-Qingdao/4D-BioReconX/blob/main/SPCAnalysis/meta-nicheanalysis/calculate-niches-on-coords.ipynb)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "When considering *niches*, we always say surrounding cellular or molecular component of a target cell. However, focusing on only a single cell would never make sense in reference of any biology process, which prompt us to group cells with similar state and ask what elements may trigger the activate of this target cell group. \n", "\n", "The following tutorial descibes a demo example for calculating surrounding cellular component of our target cell group *c3*, which represent neoblast cells in our paper. In this calculation, we used both distance and count of neighbor cells to infer the main ingredient of local microenvironment." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import niche\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "we have included a demo file for testing, you can find with name 'demo.txt'. In this file, each line represent a cell with its spatial coordinates **x**, **y** and cell categories **cluster**" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | x | \n", "y | \n", "cluster | \n", "
|---|---|---|---|
| cell | \n", "\n", " | \n", " | \n", " |
| -23531.WT_25 | \n", "2353.578947 | \n", "1708.157895 | \n", "c34 | \n", "
| -23493.WT_25 | \n", "2642.612903 | \n", "1682.451613 | \n", "c9 | \n", "
| -23480.WT_25 | \n", "2546.903226 | \n", "1683.193548 | \n", "c23 | \n", "
| -23479.WT_25 | \n", "2827.598726 | \n", "1668.636943 | \n", "c3 | \n", "
| -23380.WT_25 | \n", "2364.428571 | \n", "1671.333333 | \n", "c6 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "
| 197449.WT_25 | \n", "23.949495 | \n", "754.535354 | \n", "c18 | \n", "
| 197451.WT_25 | \n", "22.048077 | \n", "742.721154 | \n", "c18 | \n", "
| 197454.WT_25 | \n", "18.070796 | \n", "707.345133 | \n", "c18 | \n", "
| 197458.WT_25 | \n", "16.148760 | \n", "671.520661 | \n", "c17 | \n", "
| 197460.WT_25 | \n", "17.311688 | \n", "747.246753 | \n", "c18 | \n", "
61743 rows × 3 columns
\n", "| \n", " | group | \n", "count | \n", "max_dens | \n", "nearest_dist | \n", "
|---|---|---|---|---|
| 0 | \n", "c2 | \n", "2005 | \n", "0.001833 | \n", "16.892981 | \n", "
| 1 | \n", "c6 | \n", "865 | \n", "0.001893 | \n", "19.650777 | \n", "
| 2 | \n", "c22 | \n", "666 | \n", "0.001836 | \n", "21.152721 | \n", "
| 3 | \n", "c12 | \n", "568 | \n", "0.001858 | \n", "14.197462 | \n", "
| 4 | \n", "c9 | \n", "550 | \n", "0.001718 | \n", "22.821707 | \n", "
| 5 | \n", "c7 | \n", "491 | \n", "0.001740 | \n", "17.173243 | \n", "
| 6 | \n", "c0 | \n", "486 | \n", "0.001809 | \n", "9.406311 | \n", "
| 7 | \n", "c11 | \n", "375 | \n", "0.001620 | \n", "11.316524 | \n", "
| 8 | \n", "c10 | \n", "355 | \n", "0.001631 | \n", "16.539270 | \n", "
| 9 | \n", "c17 | \n", "326 | \n", "0.001978 | \n", "9.196763 | \n", "
| 10 | \n", "c1 | \n", "258 | \n", "0.001980 | \n", "10.156676 | \n", "
| 11 | \n", "c14 | \n", "230 | \n", "0.001634 | \n", "17.060274 | \n", "
| 12 | \n", "c27 | \n", "164 | \n", "0.001833 | \n", "10.452174 | \n", "
| 13 | \n", "c8 | \n", "151 | \n", "0.001927 | \n", "5.927211 | \n", "
| 14 | \n", "c23 | \n", "149 | \n", "0.001828 | \n", "7.633153 | \n", "
| 15 | \n", "c26 | \n", "138 | \n", "0.002363 | \n", "10.413944 | \n", "
| 16 | \n", "c13 | \n", "126 | \n", "0.001800 | \n", "3.258554 | \n", "
| 17 | \n", "c29 | \n", "101 | \n", "0.002025 | \n", "0.504831 | \n", "
| 18 | \n", "c30 | \n", "93 | \n", "0.001979 | \n", "6.310088 | \n", "
| 19 | \n", "c21 | \n", "93 | \n", "0.001734 | \n", "29.317459 | \n", "
| 20 | \n", "c32 | \n", "89 | \n", "0.002039 | \n", "0.040527 | \n", "
| 21 | \n", "c16 | \n", "64 | \n", "0.001660 | \n", "0.494309 | \n", "