{ "cells": [ { "cell_type": "markdown", "id": "43219aeb-d563-42a3-9221-f9cb16cfffb2", "metadata": {}, "source": [ "# Comparative Analysis\n", "\n", "In scientific research, comparing disturbed or disease samples with control samples allows for the exploration of changes in functional mechanisms at both global and local levels. Stereopy is specifically designed to identify global and local diversities in comparative samples by employing cell-level and gene-level analysis modules, supported by novel algorithms. The cell-level analysis focuses on cell diversity in terms of cell type, cell-cell occurrence, and cell community via multi-sample comparisons. At gene level, Stereopy investigates gene diversity within cell types and cell communities, proposing the concept of constant and conditional markers [[Fang23]](https://doi.org/10.1101/2023.12.04.569485).\n", "\n", "Here we use Slide-seq mouse kidney samples to test comparative analysis [[Marshall22](https://pubmed.ncbi.nlm.nih.gov/35372810/)]. Please download [test data](http://upload.dcs.cloud:8090/share/bb6fab82-2c16-46b2-a95e-6931338f31bf), and here also offers the access to [full data](https://cellxgene.cziscience.com/collections/8e880741-bf9a-4c8e-9227-934204631d2a) from the paper." ] }, { "cell_type": "markdown", "id": "17addd94-8cb8-42d4-821e-1f3c184ef4b7", "metadata": { "execution": { "iopub.execute_input": "2023-10-18T01:45:30.640277Z", "iopub.status.busy": "2023-10-18T01:45:30.639316Z", "iopub.status.idle": "2023-10-18T01:45:30.648311Z", "shell.execute_reply": "2023-10-18T01:45:30.646683Z", "shell.execute_reply.started": "2023-10-18T01:45:30.640117Z" }, "tags": [] }, "source": [ "## Preparing data" ] }, { "cell_type": "code", "execution_count": 1, "id": "2d71904b-1847-4ca5-9cc2-1677a4aa61ee", "metadata": { "execution": { "iopub.execute_input": "2024-08-29T10:00:54.710568Z", "iopub.status.busy": "2024-08-29T10:00:54.710441Z", "iopub.status.idle": "2024-08-29T10:01:00.713211Z", "shell.execute_reply": 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"metadata": {}, "output_type": "execute_result" } ], "source": [ "ms_data = MSData(_var_type='union')\n", "data = st.io.read_h5ad('../../data/Puck_191223_19.h5ad', spatial_key='X_spatial')\n", "ms_data['WT'] = data\n", "data = st.io.read_h5ad('../../data/Puck_200104_07.h5ad', spatial_key='X_spatial')\n", "ms_data['UMOD_KI'] = data\n", "\n", "## merge data\n", "ms_data.integrate()\n", "\n", "## merged author_cell_type col to ms_data\n", "ms_data.to_integrate(res_key = 'author_cell_type', scope = slice_generator[:], _from=slice_generator[:], type='obs', item='author_cell_type')\n", "ms_data" ] }, { "cell_type": "code", "execution_count": 3, "id": "b1a8db84-5417-4f84-9faf-3905df31d1a8", "metadata": { "execution": { "iopub.execute_input": "2024-08-29T10:01:02.182709Z", "iopub.status.busy": "2024-08-29T10:01:02.182520Z", "iopub.status.idle": "2024-08-29T10:01:02.903932Z", "shell.execute_reply": "2024-08-29T10:01:02.903206Z", "shell.execute_reply.started": "2024-08-29T10:01:02.182695Z" }, 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| 22614 | \n", "-84.911546 | \n", "0.0 | \n", "0.0 | \n", "-5.308575 | \n", "ENSMUSG00000027070 | \n", "0.005983 | \n", "0.189646 | \n", "0.006182 | \n", "
| 22615 | \n", "-85.269715 | \n", "0.0 | \n", "0.0 | \n", "-5.068659 | \n", "ENSMUSG00000026730 | \n", "0.006777 | \n", "0.194399 | \n", "0.007405 | \n", "
| 22616 | \n", "-86.208055 | \n", "0.0 | \n", "0.0 | \n", "-5.330188 | \n", "ENSMUSG00000074254 | \n", "0.005818 | \n", "0.193942 | \n", "0.005884 | \n", "
9120 rows × 8 columns
\n", "