{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "ziNMon68otdy"
},
"source": [
"# Symphonypy usage with your own reference without batch"
]
},
{
"cell_type": "code",
"source": [
"!pip install scanpy[leiden] openTSNE symphonypy\n",
"!gdown \"1jW548g6ERFS0t7NywgyjRs6VaE5QwXbg&confirm=t\""
],
"metadata": {
"id": "nCPVMLnPIxqN"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 221
},
"id": "bsGMbgYeozIm",
"outputId": "2cc53a48-a88f-426e-85a1-1200266b8507"
},
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
" orig.ident lane donor time celltype.l1 celltype.l2 \\\n",
"L1_AAACCCATCTGCGGAC P1_0 L1 P1 0 CD4 T CD4 TCM \n",
"L1_AAACGAAAGTTACTCG P1_0 L1 P1 0 CD4 T CD4 TCM \n",
"L1_AAACGCTAGGTCGTCC P1_0 L1 P1 0 CD8 T CD8 TEM \n",
"L1_AAAGAACGTATCCTCC P1_0 L1 P1 0 CD8 T CD8 Naive \n",
"L1_AAAGAACTCGCTTAAG P1_0 L1 P1 0 CD4 T CD4 TCM \n",
"\n",
" celltype.l3 Phase \n",
"L1_AAACCCATCTGCGGAC CD4 TCM_1 S \n",
"L1_AAACGAAAGTTACTCG CD4 TCM_3 G1 \n",
"L1_AAACGCTAGGTCGTCC CD8 TEM_2 S \n",
"L1_AAAGAACGTATCCTCC CD8 Naive S \n",
"L1_AAAGAACTCGCTTAAG CD4 TCM_1 S "
],
"text/html": [
"\n",
"
| \n", " | orig.ident | \n", "lane | \n", "donor | \n", "time | \n", "celltype.l1 | \n", "celltype.l2 | \n", "celltype.l3 | \n", "Phase | \n", "
|---|---|---|---|---|---|---|---|---|
| L1_AAACCCATCTGCGGAC | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD4 T | \n", "CD4 TCM | \n", "CD4 TCM_1 | \n", "S | \n", "
| L1_AAACGAAAGTTACTCG | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD4 T | \n", "CD4 TCM | \n", "CD4 TCM_3 | \n", "G1 | \n", "
| L1_AAACGCTAGGTCGTCC | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD8 T | \n", "CD8 TEM | \n", "CD8 TEM_2 | \n", "S | \n", "
| L1_AAAGAACGTATCCTCC | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD8 T | \n", "CD8 Naive | \n", "CD8 Naive | \n", "S | \n", "
| L1_AAAGAACTCGCTTAAG | \n", "P1_0 | \n", "L1 | \n", "P1 | \n", "0 | \n", "CD4 T | \n", "CD4 TCM | \n", "CD4 TCM_1 | \n", "S | \n", "