{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Basic use 2: Human to mouse" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here is a brief demonstration on how to use TransBrain to map the phenptype from human to mouse. The example data used in this tutorial can be download from ``exampledata`` directory of our [GitHub repository](https://github.com/ibpshangzheng/transbrain/tree/main/transbrain/exampledata)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Step 1: Prepare input data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There are two ways to input data. One is that you already have region-level phenotype data as a ``CSV`` table which follows the format and region order in the [provided template file](https://github.com/ibpshangzheng/transbrain/tree/main/transbrain/exampledata). The DataFrame contains two columns: ``['Anatomical Name', 'Phenotype']``." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here we load the example human data table." ] }, { "cell_type": "code", "execution_count": 53, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "\n", "# Example human data\n", "human_phenotype = pd.read_csv('../../../transbrain/exampledata/human/bn/human_bn_all_example_data.csv',index_col=0)" ] }, { "cell_type": "code", "execution_count": 54, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | Phenotype | \n", "
|---|---|
| Anatomical Name | \n", "\n", " |
| A8m | \n", "0.260696 | \n", "
| A8dl | \n", "-0.132093 | \n", "
| A9l | \n", "-0.841146 | \n", "
| A6dl | \n", "0.151087 | \n", "
| A6m | \n", "0.614044 | \n", "
| ... | \n", "... | \n", "
| Otha | \n", "2.237752 | \n", "
| mPFtha | \n", "2.532931 | \n", "
| lPFtha | \n", "2.300108 | \n", "
| rTtha | \n", "2.957160 | \n", "
| PPtha | \n", "1.973803 | \n", "
127 rows × 1 columns
\n", "| \n", " | Anatomical Name | \n", "Atlas Index | \n", "
|---|---|---|
| 0 | \n", "A8m | \n", "1 | \n", "
| 1 | \n", "A8dl | \n", "2 | \n", "
| 2 | \n", "A9l | \n", "3 | \n", "
| 3 | \n", "A6dl | \n", "4 | \n", "
| 4 | \n", "A6m | \n", "5 | \n", "
| ... | \n", "... | \n", "... | \n", "
| 122 | \n", "rTtha | \n", "123 | \n", "
| 123 | \n", "PPtha | \n", "124 | \n", "
| 124 | \n", "Otha | \n", "125 | \n", "
| 125 | \n", "cTtha | \n", "126 | \n", "
| 126 | \n", "lPFtha | \n", "127 | \n", "
127 rows × 2 columns
\n", "| \n", " | Phenotype | \n", "
|---|---|
| Anatomical Name | \n", "\n", " |
| A8m | \n", "0.260747 | \n", "
| A8dl | \n", "-0.132129 | \n", "
| A9l | \n", "-0.841126 | \n", "
| A6dl | \n", "0.151081 | \n", "
| A6m | \n", "0.614070 | \n", "
| ... | \n", "... | \n", "
| Otha | \n", "2.237802 | \n", "
| mPFtha | \n", "2.532970 | \n", "
| lPFtha | \n", "2.300147 | \n", "
| rTtha | \n", "2.957121 | \n", "
| PPtha | \n", "1.973806 | \n", "
127 rows × 1 columns
\n", "| \n", " | Phenotype | \n", "
|---|---|
| ACAd | \n", "0.296682 | \n", "
| ACAv | \n", "0.303369 | \n", "
| PL | \n", "0.327434 | \n", "
| ILA | \n", "0.332395 | \n", "
| ORBl | \n", "0.386486 | \n", "
| ... | \n", "... | \n", "
| MTN | \n", "0.696940 | \n", "
| ILM | \n", "0.688615 | \n", "
| GENv | \n", "0.638572 | \n", "
| EPI | \n", "0.731165 | \n", "
| RT | \n", "0.640975 | \n", "
68 rows × 1 columns
\n", "