{ "cells": [ { "attachments": {}, "cell_type": "markdown", "id": "937ac162", "metadata": {}, "source": [ "# Batch Effect" ] }, { "attachments": {}, "cell_type": "markdown", "id": "35707318", "metadata": {}, "source": [ "This part shows how to integrate data of different batches. As integration works by adjusting the principal components, this function should be performed after PCA." ] }, { "attachments": {}, "cell_type": "markdown", "id": "fee5a4e2", "metadata": {}, "source": [ "## Integration" ] }, { "attachments": {}, "cell_type": "markdown", "id": "6737256d", "metadata": {}, "source": [ "### Reading data" ] }, { "attachments": {}, "cell_type": "markdown", "id": "e8d6432c", "metadata": {}, "source": [ "Two batches of experiment data stored in GEM files are uesd here, which are lasso results from their original GEF file.\n", "\n", "Please download our [example data](http://upload.dcs.cloud:8090/share/bb6fab82-2c16-46b2-a95e-6931338f31bf)." ] }, { "cell_type": "code", "execution_count": 1, "id": "3461a894-fee1-4d67-b426-c797f2e748e2", "metadata": { "ExecuteTime": { "end_time": "2023-02-13T09:10:50.924405Z", "start_time": "2023-02-13T09:06:28.613395Z" }, "execution": { "iopub.execute_input": "2024-05-08T08:01:03.801480Z", "iopub.status.busy": 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"import warnings\n", "warnings.filterwarnings('ignore')" ] }, { "cell_type": "code", "execution_count": 2, "id": "1cffc9b8-8182-483e-9735-cf1cd68ab2cf", "metadata": { "ExecuteTime": { "end_time": "2023-02-13T09:10:50.924405Z", "start_time": "2023-02-13T09:06:28.613395Z" }, "execution": { "iopub.execute_input": "2024-05-08T08:01:14.777884Z", "iopub.status.busy": "2024-05-08T08:01:14.777285Z", "iopub.status.idle": "2024-05-08T08:03:23.659780Z", "shell.execute_reply": "2024-05-08T08:03:23.658813Z", "shell.execute_reply.started": "2024-05-08T08:01:14.777858Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[2024-05-08 04:02:18][Stereo][244929][MainThread][140462125991744][reader][159][INFO]: the martrix has 10762 cells, and 24687 genes.\n", "[2024-05-08 04:03:22][Stereo][244929][MainThread][140462125991744][reader][159][INFO]: the martrix has 10464 cells, and 24966 genes.\n" ] } ], "source": [ "input_file_1 = '../data/SS200000132BR_A1.bin1.Lasso.gem.gz'\n", "input_file_2 = '../data/SS200000132BR_A2.bin1.Lasso.gem.gz'\n", "\n", "data1 = st.io.read_gem(input_file_1)\n", "data2 = st.io.read_gem(input_file_2)" ] }, { "attachments": {}, "cell_type": "markdown", "id": "292d687b", "metadata": {}, "source": [ "### Preprocessing" ] }, { "attachments": {}, "cell_type": "markdown", "id": "577590c1", "metadata": {}, "source": [ "Before integrating batches, we need to do basic preprocessing for each batch, including quality control and filtering." ] }, { "cell_type": "code", "execution_count": 3, "id": "f5d289d6", "metadata": { "ExecuteTime": { "end_time": "2023-02-13T09:10:51.527836Z", "start_time": "2023-02-13T09:10:50.928855Z" }, "execution": { "iopub.execute_input": "2024-05-08T08:03:23.661607Z", "iopub.status.busy": "2024-05-08T08:03:23.661354Z", "iopub.status.idle": "2024-05-08T08:03:24.720340Z", "shell.execute_reply": "2024-05-08T08:03:24.719616Z", "shell.execute_reply.started": "2024-05-08T08:03:23.661585Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[2024-05-08 04:03:23][Stereo][244929][MainThread][140462125991744][st_pipeline][41][INFO]: start to run cal_qc...\n", "[2024-05-08 04:03:24][Stereo][244929][MainThread][140462125991744][st_pipeline][44][INFO]: cal_qc end, consume time 0.5445s.\n", "[2024-05-08 04:03:24][Stereo][244929][MainThread][140462125991744][st_pipeline][41][INFO]: start to run cal_qc...\n", "[2024-05-08 04:03:24][Stereo][244929][MainThread][140462125991744][st_pipeline][44][INFO]: cal_qc end, consume time 0.5038s.\n" ] } ], "source": [ "data1.tl.cal_qc()\n", "data2.tl.cal_qc()" ] }, { "attachments": {}, "cell_type": "markdown", "id": "8d29bd61", "metadata": {}, "source": [ "Draw scatter plots to observe the distribution, and set appropriate parameters. Filter cells or genes by `st.tl.filter_cells` or `st.tl.filter_genes`." ] }, { "cell_type": "code", "execution_count": 4, "id": "782f27e0", "metadata": { "ExecuteTime": { "end_time": "2023-02-13T09:11:02.416339Z", "start_time": "2023-02-13T09:10:51.530537Z" }, "execution": { "iopub.execute_input": "2024-05-08T08:03:24.721538Z", "iopub.status.busy": "2024-05-08T08:03:24.721342Z", "iopub.status.idle": "2024-05-08T08:03:25.410451Z", "shell.execute_reply": "2024-05-08T08:03:25.409693Z", "shell.execute_reply.started": "2024-05-08T08:03:24.721520Z" } }, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "