{ "cells": [ { "cell_type": "markdown", "id": "4fe829bf", "metadata": {}, "source": [ "# Li et al., 2023 Datasets (DARLIN)" ] }, { "cell_type": "code", "execution_count": null, "id": "de348a17", "metadata": {}, "outputs": [], "source": [ "import cospar as cs\n", "import scanpy as sc\n", "import pandas as pd\n", "import scipy.sparse as ssp\n", "import seaborn as sns\n", "from matplotlib import pyplot as plt\n", "import numpy as np\n", "import os\n", "adata_orig=cs.hf.read(\"/home/zhengtuo/songtao/DestinyNet/tissue_adata_refined_20221106_joint.h5ad\")\n", "adata_orig" ] }, { "cell_type": "code", "execution_count": 792, "id": "a673f6f9", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Maximum value: 821.181884765625\n", "Minimum value: 0.0\n" ] } ], "source": [ "# 检查最大值和最小值\n", "max_value = np.max(adata_orig.X)\n", "min_value = np.min(adata_orig.X)\n", "\n", "print(f\"Maximum value: {max_value}\")\n", "print(f\"Minimum value: {min_value}\")" ] }, { "cell_type": "code", "execution_count": 763, "id": "ada9dd8a", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/zhengtuo/miniconda3/envs/jst/lib/python3.9/site-packages/anndata/compat/_overloaded_dict.py:106: ImplicitModificationWarning: Trying to modify attribute `._uns` of view, initializing view as actual.\n", " self.data[key] = value\n" ] } ], "source": [ "adata_orig=adata_orig[adata_orig.obs['tissue'].isin(['Skull'])]\n", "adata_orig=adata_orig[adata_orig.obs['state_info']!='Dc']\n", "adata_orig.uns['data_des']=['Skull']\n", "\n", "adata_orig.obs['cell_type']=adata_orig.obs['cell_type'].astype(str)\n", "adata_orig.obs['cell_type']=pd.Categorical(adata_orig.obs['cell_type']).set_categories(['HSC', 'MkP','Ery', 'Baso', 'Neu', 'Mon', 'LMPP'], ordered=True)\n", "adata_orig.uns['cell_type_colors']=['#d62728','#ff7f0e', '#1f77b4', '#279e68', '#aa40fc', '#8c564b', '#e377c2'] #,'#d9d9d9']\n", "adata_orig.obs['state_info']=adata_orig.obs['cell_type'].astype(str)" ] }, { "cell_type": "code", "execution_count": 764, "id": "052b5944", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Clones without any cells are removed.\n", "Time points with clonal info: ['t0' 't1']\n", "WARNING: Default ascending order of time points are: ['nan' 't0' 't1']. If not correct, run cs.hf.update_time_ordering for correction.\n", "WARNING: Please make sure that the count matrix adata.X is NOT log-transformed.\n" ] }, { "data": { "text/plain": [ "AnnData object with n_obs × n_vars = 6094 × 21406\n", " obs: 'library', 'batch', 'n_genes', 'n_counts', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'doublet_score', 'predicted_doublet', 'cell_type', 'state_info', 'time_info', 'tissue', 'state_info_old'\n", " var: 'n_cells', 'mt', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'highly_variable'\n", " uns: 'cell_type_colors', 'clonal_time_points', 'clone_id', 'data_des', 'library_colors', 'neighbors', 'scrublet', 'time_ordering', 'tissue_colors', 'umap'\n", " obsm: 'X_clone', 'X_emb', 'X_pca', 'X_umap'\n", " obsp: 'connectivities', 'distances'" ] }, "execution_count": 764, "metadata": {}, "output_type": "execute_result" } ], "source": [ "time_map={'LMPP':'t0', 'HSC':'t0', 'NA':'t1','Baso':'t1', 'MkP':'t1', 'Mon':'t1', 'Ery':'t1','Neu':'t1', 'Dc':'t1'}\n", "adata_orig.obs['time_info']=adata_orig.obs['cell_type'].map(time_map)\n", "cs.pp.initialize_adata_object(adata_orig)" ] }, { "cell_type": "code", "execution_count": 798, "id": "696ca961", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " clone_N clone_fraction\n", "state_info \n", "Baso 22 0.022893\n", "Baso,Ery 4 0.004162\n", "Baso,Ery,Neu 3 0.003122\n", "Baso,HSC 1 0.001041\n", "Baso,HSC,Neu 1 0.001041\n", "... ... ...\n", "Mon,MkP,HSC 2 0.002081\n", "Mon,MkP,LMPP,HSC 1 0.001041\n", "Mon,Neu 33 0.034339\n", "Neu 119 0.123829\n", "Neu,Mon,HSC 2 0.002081\n", "\n", "[97 rows x 2 columns]\n", "-----------\n", " cell_N clonal_cell_fraction\n", "state_info \n", "Baso 97 0.034336\n", "Ery 459 0.162478\n", "HSC 552 0.195398\n", "LMPP 197 0.069735\n", "MkP 215 0.076106\n", "Mon 573 0.202832\n", "Neu 732 0.259115\n", "add information at obs['clone_id']\n" ] } ], "source": [ "df_clone=cs.tl.clone_statistics(adata_orig,joint_variable='state_info');\n", "cs.tl.add_clone_id_for_each_cell(adata_orig)\n" ] }, { "cell_type": "code", "execution_count": 799, "id": "69377582", "metadata": { "scrolled": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/zhengtuo/miniconda3/envs/jst/lib/python3.9/site-packages/anndata/_core/anndata.py:121: ImplicitModificationWarning: Transforming to str index.\n", " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n" ] }, { "data": { "text/html": [ "
| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "state_info_old | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "clone | \n", "clone_id | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "LL837_skull | \n", "1 | \n", "2182 | \n", "10000.000000 | \n", "2182 | \n", "8330.0 | \n", "566.0 | \n", "6.794718 | \n", "0.043403 | \n", "0 | \n", "... | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 1 | \n", "LL837_skull | \n", "1 | \n", "2247 | \n", "10000.000000 | \n", "2247 | \n", "10328.0 | \n", "128.0 | \n", "1.239349 | \n", "0.048237 | \n", "0 | \n", "... | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 2 | \n", "LL837_skull | \n", "1 | \n", "4151 | \n", "9999.999023 | \n", "4150 | \n", "29156.0 | \n", "420.0 | \n", "1.440527 | \n", "0.012388 | \n", "0 | \n", "... | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 3 | \n", "LL837_skull | \n", "1 | \n", "1515 | \n", "10000.000000 | \n", "1515 | \n", "6034.0 | \n", "146.0 | \n", "2.419622 | \n", "0.146524 | \n", "0 | \n", "... | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 4 | \n", "LL837_skull | \n", "1 | \n", "1782 | \n", "10000.000000 | \n", "1782 | \n", "6942.0 | \n", "108.0 | \n", "1.555748 | \n", "0.022658 | \n", "0 | \n", "... | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 5480 | \n", "LL837_skull | \n", "1 | \n", "4018 | \n", "9999.999023 | \n", "4018 | \n", "28538.0 | \n", "532.0 | \n", "1.864181 | \n", "0.019007 | \n", "0 | \n", "... | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 5481 | \n", "LL837_skull | \n", "1 | \n", "3561 | \n", "10000.000000 | \n", "3561 | \n", "22548.0 | \n", "534.0 | \n", "2.368281 | \n", "0.015441 | \n", "0 | \n", "... | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "73 | \n", "73 | \n", "
| 5482 | \n", "LL837_skull | \n", "1 | \n", "4073 | \n", "9999.999023 | \n", "4073 | \n", "29120.0 | \n", "474.0 | \n", "1.627747 | \n", "0.019994 | \n", "0 | \n", "... | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "0 | \n", "\n", " |
| 5483 | \n", "LL837_skull | \n", "1 | \n", "3697 | \n", "10000.000977 | \n", "3697 | \n", "26760.0 | \n", "632.0 | \n", "2.361734 | \n", "0.016280 | \n", "0 | \n", "... | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "412 | \n", "412 | \n", "
| 5485 | \n", "LL837_skull | \n", "1 | \n", "3283 | \n", "9999.999023 | \n", "3283 | \n", "21940.0 | \n", "274.0 | \n", "1.248861 | \n", "0.023810 | \n", "0 | \n", "... | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "nan | \n", "344 | \n", "344 | \n", "
4919 rows × 24 columns
\n", "| \n", " | clone_id | \n", "clone_size | \n", "state_info | \n", "state_info_N | \n", "
|---|---|---|---|---|
| 0 | \n", "0 | \n", "2 | \n", "Ery,Neu | \n", "2 | \n", "
| 1 | \n", "1 | \n", "2 | \n", "nan,HSC | \n", "2 | \n", "
| 2 | \n", "2 | \n", "2 | \n", "MkP,nan | \n", "2 | \n", "
| 3 | \n", "3 | \n", "5 | \n", "Ery,Mon,Neu | \n", "3 | \n", "
| 4 | \n", "4 | \n", "1 | \n", "nan | \n", "1 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 1029 | \n", "1029 | \n", "1 | \n", "MkP | \n", "1 | \n", "
| 1030 | \n", "1030 | \n", "2 | \n", "Ery,Neu | \n", "2 | \n", "
| 1031 | \n", "1031 | \n", "2 | \n", "Ery | \n", "1 | \n", "
| 1032 | \n", "1032 | \n", "1 | \n", "LMPP | \n", "1 | \n", "
| 1033 | \n", "1033 | \n", "1 | \n", "nan | \n", "1 | \n", "
1034 rows × 4 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "tissue | \n", "state_info_old | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "index | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LL837_skull_AAACCCAAGAGTCACG | \n", "LL837_skull | \n", "1 | \n", "2182 | \n", "10000.000000 | \n", "2182 | \n", "8330.0 | \n", "566.0 | \n", "6.794718 | \n", "0.043403 | \n", "0 | \n", "... | \n", "Skull | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_AAACCCAAGTGAACAT | \n", "LL837_skull | \n", "1 | \n", "2247 | \n", "10000.000000 | \n", "2247 | \n", "10328.0 | \n", "128.0 | \n", "1.239349 | \n", "0.048237 | \n", "0 | \n", "... | \n", "Skull | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "
| LL837_skull_AAACCCACATCCGTTC | \n", "LL837_skull | \n", "1 | \n", "4151 | \n", "9999.999023 | \n", "4150 | \n", "29156.0 | \n", "420.0 | \n", "1.440527 | \n", "0.012388 | \n", "0 | \n", "... | \n", "Skull | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "2 | \n", "
| LL837_skull_AAACCCAGTCCACATA | \n", "LL837_skull | \n", "1 | \n", "1515 | \n", "10000.000000 | \n", "1515 | \n", "6034.0 | \n", "146.0 | \n", "2.419622 | \n", "0.146524 | \n", "0 | \n", "... | \n", "Skull | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "3 | \n", "
| LL837_skull_AAACCCAGTGAACGGT | \n", "LL837_skull | \n", "1 | \n", "1782 | \n", "10000.000000 | \n", "1782 | \n", "6942.0 | \n", "108.0 | \n", "1.555748 | \n", "0.022658 | \n", "0 | \n", "... | \n", "Skull | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "4 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| LL837_skull_TTTGGTTTCATGCCCT | \n", "LL837_skull | \n", "1 | \n", "4073 | \n", "9999.999023 | \n", "4073 | \n", "29120.0 | \n", "474.0 | \n", "1.627747 | \n", "0.019994 | \n", "0 | \n", "... | \n", "Skull | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5482 | \n", "
| LL837_skull_TTTGGTTTCGACGTCG | \n", "LL837_skull | \n", "1 | \n", "3697 | \n", "10000.000977 | \n", "3697 | \n", "26760.0 | \n", "632.0 | \n", "2.361734 | \n", "0.016280 | \n", "0 | \n", "... | \n", "Skull | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5483 | \n", "
| LL837_skull_TTTGTTGAGCGTTACT | \n", "LL837_skull | \n", "1 | \n", "1476 | \n", "10000.000000 | \n", "1476 | \n", "6594.0 | \n", "286.0 | \n", "4.337276 | \n", "0.079240 | \n", "0 | \n", "... | \n", "Skull | \n", "LMPP | \n", "2 | \n", "0.074549 | \n", "0.185234 | \n", "0.142106 | \n", "0.400063 | \n", "NaN | \n", "NaN | \n", "5484 | \n", "
| LL837_skull_TTTGTTGAGTGATCGG | \n", "LL837_skull | \n", "1 | \n", "3283 | \n", "9999.999023 | \n", "3283 | \n", "21940.0 | \n", "274.0 | \n", "1.248861 | \n", "0.023810 | \n", "0 | \n", "... | \n", "Skull | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5485 | \n", "
| LL837_skull_TTTGTTGGTTACAGCT | \n", "LL837_skull | \n", "1 | \n", "817 | \n", "10000.000977 | \n", "817 | \n", "2316.0 | \n", "192.0 | \n", "8.290155 | \n", "0.031239 | \n", "0 | \n", "... | \n", "Skull | \n", "LMPP | \n", "2 | \n", "0.163187 | \n", "0.226108 | \n", "0.252171 | \n", "0.273444 | \n", "NaN | \n", "NaN | \n", "5486 | \n", "
5487 rows × 23 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "state_info_old | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "Fate_binary | \n", "clone | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 13 | \n", "LL837_skull | \n", "1 | \n", "2411 | \n", "10000.000000 | \n", "2411 | \n", "10746.0 | \n", "218.0 | \n", "2.028662 | \n", "0.053785 | \n", "0 | \n", "... | \n", "HSC | \n", "1 | \n", "0.219269 | \n", "0.158679 | \n", "0.367359 | \n", "0.216678 | \n", "No MkP bias | \n", "1 | \n", "0 | \n", "988 | \n", "
| 90 | \n", "LL837_skull | \n", "1 | \n", "2774 | \n", "10000.000000 | \n", "2774 | \n", "12630.0 | \n", "222.0 | \n", "1.757720 | \n", "0.063830 | \n", "0 | \n", "... | \n", "HSC | \n", "1 | \n", "0.488377 | \n", "0.248923 | \n", "0.097766 | \n", "0.118884 | \n", "MkP bias | \n", "1 | \n", "1 | \n", "805 | \n", "
| 112 | \n", "LL837_skull | \n", "1 | \n", "2341 | \n", "10000.000000 | \n", "2341 | \n", "9946.0 | \n", "192.0 | \n", "1.930424 | \n", "0.046968 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.128018 | \n", "0.192091 | \n", "0.386379 | \n", "0.256319 | \n", "No MkP bias | \n", "0 | \n", "0 | \n", "635 | \n", "
| 138 | \n", "LL837_skull | \n", "1 | \n", "2176 | \n", "9999.999023 | \n", "2176 | \n", "9826.0 | \n", "188.0 | \n", "1.913291 | \n", "0.052323 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.539199 | \n", "0.286691 | \n", "0.107701 | \n", "0.036490 | \n", "MkP bias | \n", "0 | \n", "1 | \n", "8 | \n", "
| 264 | \n", "LL837_skull | \n", "1 | \n", "2155 | \n", "10000.000000 | \n", "2155 | \n", "8708.0 | \n", "198.0 | \n", "2.273771 | \n", "0.038168 | \n", "0 | \n", "... | \n", "HSC | \n", "1 | \n", "0.360206 | \n", "0.175236 | \n", "0.265452 | \n", "0.174175 | \n", "MkP bias | \n", "1 | \n", "1 | \n", "444 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 5256 | \n", "LL837_skull | \n", "1 | \n", "1697 | \n", "10000.000000 | \n", "1697 | \n", "7322.0 | \n", "124.0 | \n", "1.693526 | \n", "0.081879 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.348092 | \n", "0.132318 | \n", "0.414731 | \n", "0.042925 | \n", "MkP bias | \n", "0 | \n", "1 | \n", "251 | \n", "
| 5279 | \n", "LL837_skull | \n", "1 | \n", "1293 | \n", "10000.000977 | \n", "1293 | \n", "4532.0 | \n", "130.0 | \n", "2.868491 | \n", "0.090645 | \n", "0 | \n", "... | \n", "HSC | \n", "1 | \n", "0.395193 | \n", "0.151719 | \n", "0.306524 | \n", "0.107999 | \n", "MkP bias | \n", "1 | \n", "1 | \n", "777 | \n", "
| 5357 | \n", "LL837_skull | \n", "1 | \n", "1799 | \n", "10000.000000 | \n", "1799 | \n", "6732.0 | \n", "130.0 | \n", "1.931075 | \n", "0.028299 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.426256 | \n", "0.188785 | \n", "0.268747 | \n", "0.079448 | \n", "MkP bias | \n", "0 | \n", "1 | \n", "170 | \n", "
| 5398 | \n", "LL837_skull | \n", "1 | \n", "1944 | \n", "10000.000000 | \n", "1944 | \n", "7712.0 | \n", "140.0 | \n", "1.815353 | \n", "0.053785 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.159331 | \n", "0.248843 | \n", "0.387131 | \n", "0.148377 | \n", "No MkP bias | \n", "0 | \n", "0 | \n", "272 | \n", "
| 5418 | \n", "LL837_skull | \n", "1 | \n", "2737 | \n", "10000.000000 | \n", "2737 | \n", "11318.0 | \n", "218.0 | \n", "1.926135 | \n", "0.039152 | \n", "0 | \n", "... | \n", "HSC | \n", "0 | \n", "0.326030 | \n", "0.129297 | \n", "0.297700 | \n", "0.219458 | \n", "MkP bias | \n", "0 | \n", "1 | \n", "8 | \n", "
68 rows × 24 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "time_info | \n", "tissue | \n", "state_info_old | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LL837_skull_AAAGGATCACGTTGGC | \n", "LL837_skull | \n", "1 | \n", "4425 | \n", "10000.000000 | \n", "4425 | \n", "42134.0 | \n", "766.0 | \n", "1.818009 | \n", "0.011020 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Ery | \n", "0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_AACCTGACATGGATCT | \n", "LL837_skull | \n", "1 | \n", "3366 | \n", "10000.000000 | \n", "3366 | \n", "18584.0 | \n", "396.0 | \n", "2.130865 | \n", "0.060215 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Mon | \n", "0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_AAGTGAATCAGTGTCA | \n", "LL837_skull | \n", "1 | \n", "3013 | \n", "10000.000977 | \n", "3013 | \n", "16668.0 | \n", "542.0 | \n", "3.251740 | \n", "0.061986 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Meg | \n", "1 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "
| LL837_skull_ACAAAGAAGAGGCGTT | \n", "LL837_skull | \n", "1 | \n", "3105 | \n", "9999.999023 | \n", "3105 | \n", "16682.0 | \n", "290.0 | \n", "1.738401 | \n", "0.035385 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Meg | \n", "1 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "
| LL837_skull_ACACGCGTCAACCTTT | \n", "LL837_skull | \n", "1 | \n", "3517 | \n", "9999.999023 | \n", "3517 | \n", "21620.0 | \n", "308.0 | \n", "1.424607 | \n", "0.040166 | \n", "0 | \n", "... | \n", "t0 | \n", "Skull | \n", "LMPP | \n", "0 | \n", "0.035840 | \n", "0.210532 | \n", "0.120582 | \n", "0.455573 | \n", "NaN | \n", "0 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| LL837_skull_TTCTTCCTCATTTCCA | \n", "LL837_skull | \n", "1 | \n", "4472 | \n", "9999.999023 | \n", "4471 | \n", "26352.0 | \n", "434.0 | \n", "1.646934 | \n", "0.018529 | \n", "0 | \n", "... | \n", "t0 | \n", "Skull | \n", "LMPP | \n", "1 | \n", "0.198727 | \n", "0.231416 | \n", "0.222007 | \n", "0.262037 | \n", "NaN | \n", "1 | \n", "
| LL837_skull_TTGCTGCAGTGCCAGA | \n", "LL837_skull | \n", "1 | \n", "4291 | \n", "9999.999023 | \n", "4290 | \n", "23722.0 | \n", "282.0 | \n", "1.188770 | \n", "0.019495 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Meg | \n", "1 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "
| LL837_skull_TTGGATGAGATGACAT | \n", "LL837_skull | \n", "1 | \n", "4844 | \n", "10000.000000 | \n", "4844 | \n", "48688.0 | \n", "816.0 | \n", "1.675978 | \n", "0.005157 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Ery | \n", "0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_TTTACGTAGAAGGATG | \n", "LL837_skull | \n", "1 | \n", "5299 | \n", "10000.000000 | \n", "5298 | \n", "38142.0 | \n", "1538.0 | \n", "4.032300 | \n", "0.010055 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Ery | \n", "0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_TTTATGCAGCAACTTC | \n", "LL837_skull | \n", "1 | \n", "2036 | \n", "9999.998047 | \n", "2036 | \n", "8584.0 | \n", "112.0 | \n", "1.304753 | \n", "0.053785 | \n", "0 | \n", "... | \n", "t1 | \n", "Skull | \n", "Ery | \n", "0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
112 rows × 22 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "tissue | \n", "state_info_old | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "index | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LL837_skull_AAACCCAAGAGTCACG | \n", "LL837_skull | \n", "1 | \n", "2182 | \n", "10000.000000 | \n", "2182 | \n", "8330.0 | \n", "566.0 | \n", "6.794718 | \n", "0.043403 | \n", "0 | \n", "... | \n", "Skull | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "
| LL837_skull_AAACCCAAGTGAACAT | \n", "LL837_skull | \n", "1 | \n", "2247 | \n", "10000.000000 | \n", "2247 | \n", "10328.0 | \n", "128.0 | \n", "1.239349 | \n", "0.048237 | \n", "0 | \n", "... | \n", "Skull | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "
| LL837_skull_AAACCCACATCCGTTC | \n", "LL837_skull | \n", "1 | \n", "4151 | \n", "9999.999023 | \n", "4150 | \n", "29156.0 | \n", "420.0 | \n", "1.440527 | \n", "0.012388 | \n", "0 | \n", "... | \n", "Skull | \n", "Mon | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "2 | \n", "
| LL837_skull_AAACCCAGTCCACATA | \n", "LL837_skull | \n", "1 | \n", "1515 | \n", "10000.000000 | \n", "1515 | \n", "6034.0 | \n", "146.0 | \n", "2.419622 | \n", "0.146524 | \n", "0 | \n", "... | \n", "Skull | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "3 | \n", "
| LL837_skull_AAACCCAGTGAACGGT | \n", "LL837_skull | \n", "1 | \n", "1782 | \n", "10000.000000 | \n", "1782 | \n", "6942.0 | \n", "108.0 | \n", "1.555748 | \n", "0.022658 | \n", "0 | \n", "... | \n", "Skull | \n", "Meg | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "4 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| LL837_skull_TTTGGTTTCATGCCCT | \n", "LL837_skull | \n", "1 | \n", "4073 | \n", "9999.999023 | \n", "4073 | \n", "29120.0 | \n", "474.0 | \n", "1.627747 | \n", "0.019994 | \n", "0 | \n", "... | \n", "Skull | \n", "Ery | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5482 | \n", "
| LL837_skull_TTTGGTTTCGACGTCG | \n", "LL837_skull | \n", "1 | \n", "3697 | \n", "10000.000977 | \n", "3697 | \n", "26760.0 | \n", "632.0 | \n", "2.361734 | \n", "0.016280 | \n", "0 | \n", "... | \n", "Skull | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5483 | \n", "
| LL837_skull_TTTGTTGAGCGTTACT | \n", "LL837_skull | \n", "1 | \n", "1476 | \n", "10000.000000 | \n", "1476 | \n", "6594.0 | \n", "286.0 | \n", "4.337276 | \n", "0.079240 | \n", "0 | \n", "... | \n", "Skull | \n", "LMPP | \n", "2 | \n", "0.074549 | \n", "0.185234 | \n", "0.142106 | \n", "0.400063 | \n", "NaN | \n", "NaN | \n", "5484 | \n", "
| LL837_skull_TTTGTTGAGTGATCGG | \n", "LL837_skull | \n", "1 | \n", "3283 | \n", "9999.999023 | \n", "3283 | \n", "21940.0 | \n", "274.0 | \n", "1.248861 | \n", "0.023810 | \n", "0 | \n", "... | \n", "Skull | \n", "Neu | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5485 | \n", "
| LL837_skull_TTTGTTGGTTACAGCT | \n", "LL837_skull | \n", "1 | \n", "817 | \n", "10000.000977 | \n", "817 | \n", "2316.0 | \n", "192.0 | \n", "8.290155 | \n", "0.031239 | \n", "0 | \n", "... | \n", "Skull | \n", "LMPP | \n", "2 | \n", "0.163187 | \n", "0.226108 | \n", "0.252171 | \n", "0.273444 | \n", "NaN | \n", "NaN | \n", "5486 | \n", "
5487 rows × 23 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "cell_type | \n", "state_info | \n", "time_info | \n", "tissue | \n", "state_info_old | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LL837_LF_AAACCCATCTTCGGTC | \n", "LL837_LF | \n", "0 | \n", "1146 | \n", "10000.001953 | \n", "1146 | \n", "3210.0 | \n", "16.0 | \n", "0.498442 | \n", "0.038168 | \n", "0 | \n", "HSC | \n", "HSC | \n", "HSC | \n", "LF | \n", "HSC | \n", "
| LL837_LF_AAACGAAGTTGTGCCG | \n", "LL837_LF | \n", "0 | \n", "3678 | \n", "10000.000000 | \n", "3677 | \n", "19478.0 | \n", "336.0 | \n", "1.725023 | \n", "0.039152 | \n", "0 | \n", "HSC | \n", "HSC | \n", "HSC | \n", "LF | \n", "HSC | \n", "
| LL837_LF_AAACGAATCGAGATAA | \n", "LL837_LF | \n", "0 | \n", "6453 | \n", "10000.000000 | \n", "6453 | \n", "60940.0 | \n", "1362.0 | \n", "2.234985 | \n", "0.015856 | \n", "0 | \n", "HSC | \n", "HSC | \n", "HSC | \n", "LF | \n", "HSC | \n", "
| LL837_LF_AAACGCTTCCATATGG | \n", "LL837_LF | \n", "0 | \n", "4972 | \n", "10000.000000 | \n", "4972 | \n", "33454.0 | \n", "700.0 | \n", "2.092425 | \n", "0.028299 | \n", "0 | \n", "HSC | \n", "HSC | \n", "HSC | \n", "LF | \n", "HSC | \n", "
| LL837_LF_AAACGCTTCGGAATGG | \n", "LL837_LF | \n", "0 | \n", "5806 | \n", "10000.000000 | \n", "5805 | \n", "46320.0 | \n", "1076.0 | \n", "2.322971 | \n", "0.036286 | \n", "0 | \n", "HSC | \n", "HSC | \n", "HSC | \n", "LF | \n", "HSC | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| LL837_spleen_TTTGGAGTCGAACACT | \n", "LL837_spleen | \n", "2 | \n", "3637 | \n", "10000.000000 | \n", "3637 | \n", "20822.0 | \n", "250.0 | \n", "1.200653 | \n", "0.032829 | \n", "0 | \n", "Ery | \n", "Ery | \n", "Ery | \n", "Spleen | \n", "Ery | \n", "
| LL837_spleen_TTTGGTTCACGATAGG | \n", "LL837_spleen | \n", "2 | \n", "3173 | \n", "9999.999023 | \n", "3173 | \n", "15726.0 | \n", "190.0 | \n", "1.208190 | \n", "0.013109 | \n", "0 | \n", "Ery | \n", "Ery | \n", "Ery | \n", "Spleen | \n", "Ery | \n", "
| LL837_spleen_TTTGGTTCAGCAGTCC | \n", "LL837_spleen | \n", "2 | \n", "6974 | \n", "10000.000977 | \n", "6974 | \n", "106512.0 | \n", "3098.0 | \n", "2.908592 | \n", "0.015034 | \n", "0 | \n", "Ery | \n", "Ery | \n", "Ery | \n", "Spleen | \n", "Ery | \n", "
| LL837_spleen_TTTGTTGCACCCATAA | \n", "LL837_spleen | \n", "2 | \n", "3348 | \n", "9999.999023 | \n", "3348 | \n", "17774.0 | \n", "280.0 | \n", "1.575335 | \n", "0.034509 | \n", "0 | \n", "Ery | \n", "Ery | \n", "Ery | \n", "Spleen | \n", "Ery | \n", "
| LL837_spleen_TTTGTTGGTCACTTAG | \n", "LL837_spleen | \n", "2 | \n", "6442 | \n", "10000.000977 | \n", "6442 | \n", "78968.0 | \n", "1528.0 | \n", "1.934961 | \n", "0.003584 | \n", "0 | \n", "Ery | \n", "Ery | \n", "Ery | \n", "Spleen | \n", "Ery | \n", "
7226 rows × 15 columns
\n", "| \n", " | library | \n", "batch | \n", "n_genes | \n", "n_counts | \n", "n_genes_by_counts | \n", "total_counts | \n", "total_counts_mt | \n", "pct_counts_mt | \n", "doublet_score | \n", "predicted_doublet | \n", "... | \n", "fate | \n", "fate_map_transition_map_MkP | \n", "fate_map_transition_map_Ery | \n", "fate_map_transition_map_Neu | \n", "fate_map_transition_map_Mon | \n", "Fate_bias | \n", "GT | \n", "index | \n", "clone | \n", "fate_pred | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "LL837_skull | \n", "1 | \n", "2182 | \n", "10000.000000 | \n", "2182 | \n", "8330.0 | \n", "566.0 | \n", "6.794718 | \n", "0.043403 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0 | \n", "0 | \n", "NaN | \n", "
| 1 | \n", "LL837_skull | \n", "1 | \n", "2247 | \n", "10000.000000 | \n", "2247 | \n", "10328.0 | \n", "128.0 | \n", "1.239349 | \n", "0.048237 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "1 | \n", "0 | \n", "NaN | \n", "
| 2 | \n", "LL837_skull | \n", "1 | \n", "4151 | \n", "9999.999023 | \n", "4150 | \n", "29156.0 | \n", "420.0 | \n", "1.440527 | \n", "0.012388 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "2 | \n", "0 | \n", "NaN | \n", "
| 3 | \n", "LL837_skull | \n", "1 | \n", "1515 | \n", "10000.000000 | \n", "1515 | \n", "6034.0 | \n", "146.0 | \n", "2.419622 | \n", "0.146524 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "3 | \n", "0 | \n", "NaN | \n", "
| 4 | \n", "LL837_skull | \n", "1 | \n", "1782 | \n", "10000.000000 | \n", "1782 | \n", "6942.0 | \n", "108.0 | \n", "1.555748 | \n", "0.022658 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "4 | \n", "0 | \n", "NaN | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 5480 | \n", "LL837_skull | \n", "1 | \n", "4018 | \n", "9999.999023 | \n", "4018 | \n", "28538.0 | \n", "532.0 | \n", "1.864181 | \n", "0.019007 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5480 | \n", "0 | \n", "NaN | \n", "
| 5481 | \n", "LL837_skull | \n", "1 | \n", "3561 | \n", "10000.000000 | \n", "3561 | \n", "22548.0 | \n", "534.0 | \n", "2.368281 | \n", "0.015441 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5481 | \n", "73 | \n", "NaN | \n", "
| 5482 | \n", "LL837_skull | \n", "1 | \n", "4073 | \n", "9999.999023 | \n", "4073 | \n", "29120.0 | \n", "474.0 | \n", "1.627747 | \n", "0.019994 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5482 | \n", "0 | \n", "NaN | \n", "
| 5483 | \n", "LL837_skull | \n", "1 | \n", "3697 | \n", "10000.000977 | \n", "3697 | \n", "26760.0 | \n", "632.0 | \n", "2.361734 | \n", "0.016280 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5483 | \n", "412 | \n", "NaN | \n", "
| 5485 | \n", "LL837_skull | \n", "1 | \n", "3283 | \n", "9999.999023 | \n", "3283 | \n", "21940.0 | \n", "274.0 | \n", "1.248861 | \n", "0.023810 | \n", "0 | \n", "... | \n", "2 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "5485 | \n", "344 | \n", "NaN | \n", "
4919 rows × 25 columns
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