{ "cells": [ { "cell_type": "markdown", "id": "3547e78d", "metadata": {}, "source": [ "# Quick Demo: Reference-based simulation for CODEX spatial proteomics data" ] }, { "cell_type": "code", "execution_count": null, "id": "a7413f0f", "metadata": {}, "outputs": [], "source": [ "import simspace as ss\n", "import pandas as pd" ] }, { "cell_type": "code", "execution_count": 2, "id": "725ed3ce", "metadata": {}, "outputs": [], "source": [ "# Step 1: Load the reference dataset. We here provide a sample dataset from Xenium human breast tumor dataset.\n", "ref_meta = pd.read_csv('../data/CODEX_metadata.csv', index_col=0)\n", "ref_omics = pd.read_csv('../data/CODEX_count.csv', index_col=0)" ] }, { "cell_type": "code", "execution_count": 3, "id": "44423533", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | Unnamed: 0.2 | \n", "Unnamed: 0.1 | \n", "Unnamed: 0 | \n", "CellID | \n", "centroid_x | \n", "centroid_y | \n", "Area | \n", "perimeter | \n", "axis_ratio | \n", "tile_h | \n", "... | \n", "IFNG | \n", "Ki67 | \n", "CD44 | \n", "PD1 | \n", "TIM3 | \n", "necrosis_2clusters | \n", "necrosis_3clusters | \n", "peri_intra_tumoral | \n", "X_centroid | \n", "Y_centroid | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| 876849 | \n", "876849 | \n", "876849 | \n", "3790987 | \n", "1 | \n", "39.842857 | \n", "2.228571 | \n", "70.0 | \n", "32.863961 | \n", "2.111366 | \n", "37888 | \n", "... | \n", "N | \n", "N | \n", "N | \n", "N | \n", "N | \n", "0 | \n", "0 | \n", "peri | \n", "37927.842857 | \n", "26882.228571 | \n", "
| 876850 | \n", "876850 | \n", "876850 | \n", "3790988 | \n", "2 | \n", "81.000000 | \n", "1.500000 | \n", "28.0 | \n", "18.000000 | \n", "1.788854 | \n", "37888 | \n", "... | \n", "N | \n", "N | \n", "N | \n", "N | \n", "N | \n", "0 | \n", "0 | \n", "peri | \n", "37969.000000 | \n", "26881.500000 | \n", "
| 876851 | \n", "876851 | \n", "876851 | \n", "3790989 | \n", "3 | \n", "94.694118 | \n", "3.058824 | \n", "85.0 | \n", "34.485281 | \n", "1.467060 | \n", "37888 | \n", "... | \n", "N | \n", "N | \n", "N | \n", "N | \n", "N | \n", "0 | \n", "0 | \n", "peri | \n", "37982.694118 | \n", "26883.058824 | \n", "
3 rows × 26 columns
\n", "| \n", " | DAPI | \n", "MPO | \n", "Ecadherin | \n", "PDL1 | \n", "CD163 | \n", "PD1 | \n", "CD47 | \n", "GAL3 | \n", "PARP1 | \n", "LAG3 | \n", "... | \n", "MLH1 | \n", "Ki67 | \n", "CD20 | \n", "ARID1A | \n", "IFNG | \n", "CD31 | \n", "PMS | \n", "CD44 | \n", "PanCytokeratin | \n", "CD3e | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CellID | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
| 1 | \n", "21.585714 | \n", "0.028571 | \n", "0.1 | \n", "0.928571 | \n", "0.014286 | \n", "1.214286 | \n", "1.128571 | \n", "32.971428 | \n", "5.657143 | \n", "1.900000 | \n", "... | \n", "24.314285 | \n", "0.900000 | \n", "5.000000 | \n", "7.657143 | \n", "0.900000 | \n", "0.400000 | \n", "1.814286 | \n", "2.828571 | \n", "1.685714 | \n", "20.142857 | \n", "
| 2 | \n", "20.071428 | \n", "0.000000 | \n", "0.0 | \n", "0.178571 | \n", "0.428571 | \n", "0.392857 | \n", "0.607143 | \n", "14.000000 | \n", "0.071429 | \n", "1.428571 | \n", "... | \n", "5.678571 | \n", "0.857143 | \n", "1.928571 | \n", "0.678571 | \n", "0.678571 | \n", "0.142857 | \n", "0.142857 | \n", "2.821429 | \n", "1.928571 | \n", "1.500000 | \n", "
| 3 | \n", "17.858824 | \n", "0.000000 | \n", "0.0 | \n", "0.047059 | \n", "0.000000 | \n", "0.235294 | \n", "0.058824 | \n", "7.482353 | \n", "0.564706 | \n", "1.364706 | \n", "... | \n", "6.764706 | \n", "0.329412 | \n", "1.835294 | \n", "1.141176 | \n", "0.458824 | \n", "0.082353 | \n", "0.200000 | \n", "0.741176 | \n", "1.635294 | \n", "0.717647 | \n", "
3 rows × 31 columns
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