{ "cells": [ { "cell_type": "markdown", "id": "3547e78d", "metadata": {}, "source": [ "# Quick Demo: Reference-based simulation for Xenium spatial transcriptomics data" ] }, { "cell_type": "code", "execution_count": 1, "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/reference_metadata.csv', index_col=0)\n", "ref_omics = pd.read_csv('../data/reference_count.csv', index_col=0)" ] }, { "cell_type": "code", "execution_count": 3, "id": "44423533", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | cell_id | \n", "x_centroid | \n", "y_centroid | \n", "transcript_counts | \n", "control_probe_counts | \n", "control_codeword_counts | \n", "total_counts | \n", "cell_area | \n", "nucleus_area | \n", "Cluster | \n", "
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "4303 | \n", "1654.367181 | \n", "2017.908301 | \n", "416 | \n", "0 | \n", "0 | \n", "416 | \n", "490.216250 | \n", "82.184375 | \n", "Stromal | \n", "
| 1 | \n", "4304 | \n", "1669.259509 | \n", "2026.475952 | \n", "560 | \n", "1 | \n", "0 | \n", "561 | \n", "348.741719 | \n", "110.226406 | \n", "Invasive_Tumor | \n", "
| 2 | \n", "4305 | \n", "1660.068158 | \n", "2040.800818 | \n", "315 | \n", "0 | \n", "0 | \n", "315 | \n", "256.668125 | \n", "65.702344 | \n", "Invasive_Tumor | \n", "
| \n", " | 4303 | \n", "4304 | \n", "4305 | \n", "4306 | \n", "4307 | \n", "4308 | \n", "4309 | \n", "4310 | \n", "4311 | \n", "4312 | \n", "... | \n", "76380 | \n", "76381 | \n", "76382 | \n", "76383 | \n", "76384 | \n", "76385 | \n", "76386 | \n", "76387 | \n", "76388 | \n", "76389 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ABCC11 | \n", "0 | \n", "16 | \n", "4 | \n", "5 | \n", "2 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "1 | \n", "2 | \n", "5 | \n", "3 | \n", "7 | \n", "3 | \n", "1 | \n", "1 | \n", "5 | \n", "
| ACTA2 | \n", "13 | \n", "2 | \n", "1 | \n", "0 | \n", "2 | \n", "0 | \n", "1 | \n", "3 | \n", "4 | \n", "13 | \n", "... | \n", "5 | \n", "0 | \n", "0 | \n", "1 | \n", "1 | \n", "0 | \n", "2 | \n", "2 | \n", "0 | \n", "0 | \n", "
| ACTG2 | \n", "1 | \n", "1 | \n", "1 | \n", "0 | \n", "2 | \n", "2 | \n", "3 | \n", "6 | \n", "2 | \n", "4 | \n", "... | \n", "1 | \n", "2 | \n", "0 | \n", "4 | \n", "1 | \n", "2 | \n", "3 | \n", "1 | \n", "1 | \n", "4 | \n", "
3 rows × 2032 columns
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