{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/data/pinello/SHARED_SOFTWARE/anaconda3/envs/huidong_py3/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace.\n", " from pandas.core.index import RangeIndex\n" ] } ], "source": [ "import numpy as np\n", "import pandas as pd\n", "import scanpy as sc" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "scanpy==1.4.6 anndata==0.7.1 umap==0.3.10 numpy==1.18.2 scipy==1.4.1 pandas==1.0.3 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.0 louvain==0.6.1\n" ] } ], "source": [ "sc.settings.verbosity = 3 # verbosity: errors (0), warnings (1), info (2), hints (3)\n", "sc.logging.print_versions()\n", "results_file = './write/Thienpont_Fibroblast.h5ad' # the file that will store the analysis results" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "sc.settings.set_figure_params(dpi=80)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "adata = sc.read_loom('../Thienpont_Fibroblast_v4_R_fixed.loom',validate=False) " ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/plain": [ "AnnData object with n_obs × n_vars = 1465 × 33694 \n", " obs: 'ClusterID', 'ClusterName', 'Clusterings', 'Embedding', 'Embeddings_X', 'Embeddings_Y', 'RegulonsAUC'\n", " var: 'Regulons'" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "adata" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | ClusterID | \n", "ClusterName | \n", "Clusterings | \n", "Embedding | \n", "Embeddings_X | \n", "Embeddings_Y | \n", "RegulonsAUC | \n", "
---|---|---|---|---|---|---|---|
AACGGTACCTTCGC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-13.224176055406895, 7.3742064782818835) | \n", "(-13.224176055406895,) | \n", "(7.3742064782818835,) | \n", "(0.0, 0.0, 0.006034328625067048, 0.00720646824... | \n", "
AGAGAAACGCCCTT_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-7.91514492205289, 8.78283568140982) | \n", "(-7.91514492205289,) | \n", "(8.78283568140982,) | \n", "(0.0, 0.0, 0.007084748793134275, 0.00829036794... | \n", "
AGGCAGGACGAATC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.000853866325636, 10.26263029622456) | \n", "(-12.000853866325636,) | \n", "(10.26263029622456,) | \n", "(0.0, 0.0, 0.006451516776923535, 0.00674751972... | \n", "
ATACCTTGCCGATA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.286540150823196, 10.915970964194518) | \n", "(-12.286540150823196,) | \n", "(10.915970964194518,) | \n", "(0.004369138959931799, 0.0, 0.0048125633232016... | \n", "
ATAGGCTGGCTTCC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-9.53959055938284, 9.796753723289438) | \n", "(-9.53959055938284,) | \n", "(9.796753723289438,) | \n", "(0.0033034953111679456, 0.0, 0.005393646820430... | \n", "
CAAAGCTGCCTCAC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.695448248947672, 9.11992887457319) | \n", "(-12.695448248947672,) | \n", "(9.11992887457319,) | \n", "(0.0, 0.0, 0.006183324393587222, 0.00645457386... | \n", "
CACTGAGAATGGTC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-16.53531856795478, 8.383207449001237) | \n", "(-16.53531856795478,) | \n", "(8.383207449001237,) | \n", "(0.0, 0.0, 0.006384468681089457, 0.00586868213... | \n", "
CAGTGTGATAGACC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-10.660643135907463, 6.339232060779948) | \n", "(-10.660643135907463,) | \n", "(6.339232060779948,) | \n", "(0.0, 0.0, 0.00860450563204005, 0.009081321771... | \n", "
CGTAACGAGCTGTA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-18.560629856607353, 6.143991391639514) | \n", "(-18.560629856607353,) | \n", "(6.143991391639514,) | \n", "(0.0, 0.0, 0.004454973478753204, 0.00457972033... | \n", "
GAAGTCTGTAGAGA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-17.730024078646018, 8.438946636054837) | \n", "(-17.730024078646018,) | \n", "(8.438946636054837,) | \n", "(0.0, 0.0, 0.007829727635735145, 0.00757753300... | \n", "
GCGTAATGACTACG_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-7.93505501420688, 6.737894666255463) | \n", "(-7.93505501420688,) | \n", "(6.737894666255463,) | \n", "(0.0, 0.0, 0.008291614518147685, 0.00984298101... | \n", "
GGGACCTGCCAATG_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.483210354994391, 10.665262830276024) | \n", "(-12.483210354994391,) | \n", "(10.665262830276024,) | \n", "(0.0, 0.0, 0.007829727635735145, 0.00862237325... | \n", "
TAGTAAACGGTATC_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-8.218587186390907, 9.245169211496469) | \n", "(-8.218587186390907,) | \n", "(9.245169211496469,) | \n", "(0.0, 0.0, 0.006332320162107396, 0.00729435200... | \n", "
TCAGTGGAGGAGCA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-15.689102994537837, 10.778876648742505) | \n", "(-15.689102994537837,) | \n", "(10.778876648742505,) | \n", "(0.0, 0.0, 0.0057363370880267, 0.0062885712053... | \n", "
TGCTATACGCGAAG_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-11.989632304629362, 7.789819486211407) | \n", "(-11.989632304629362,) | \n", "(7.789819486211407,) | \n", "(0.0, 0.0, 0.007658382501936945, 0.00893484883... | \n", "
TGGAACTGAGAACA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-18.472289966707677, 10.585948100872066) | \n", "(-18.472289966707677,) | \n", "(10.585948100872066,) | \n", "(0.0, 0.0, 0.0058927826449728824, 0.0063959846... | \n", "
TGGACCCTTCCAGA_1 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-10.453077671518598, 7.9547685788450595) | \n", "(-10.453077671518598,) | \n", "(7.9547685788450595,) | \n", "(0.0, 0.0, 0.006548364026461648, 0.00752870869... | \n", "
GGATAGCTAGTGCT_2 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(-3.8415844394962533, 7.374408897437646) | \n", "(-3.8415844394962533,) | \n", "(7.374408897437646,) | \n", "(0.0, 0.0, 0.005065856129685917, 0.00664010624... | \n", "
ACCTATTGCTGAGT_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-9.594822207312884, 9.769429213516382) | \n", "(-9.594822207312884,) | \n", "(9.769429213516382,) | \n", "(0.0, 0.0, 0.004790213957923595, 0.00627880634... | \n", "
ACGCTGCTAACCAC_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-4.032228987760553, -1.7371376298541459) | \n", "(-4.032228987760553,) | \n", "(-1.7371376298541459,) | \n", "(0.0, 0.0, 0.003851540616246499, 0.00413053667... | \n", "
ACTTCCCTAATCGC_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.714992348451274, 8.74869817404203) | \n", "(-12.714992348451274,) | \n", "(8.74869817404203,) | \n", "(0.012681159420289856, 0.0, 0.0046486679778294... | \n", "
AGACACTGCTATGG_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-16.678624314837926, 7.58475831460795) | \n", "(-16.678624314837926,) | \n", "(7.58475831460795,) | \n", "(0.0, 0.0, 0.004305977710233029, 0.00520467151... | \n", "
AGCTCGCTGTACGT_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-0.6321711421803933, -0.4111997346453388) | \n", "(-0.6321711421803933,) | \n", "(-0.4111997346453388,) | \n", "(0.0, 0.0, 0.004052684903748734, 0.00531208499... | \n", "
ATAGGCTGCTCAGA_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-12.044312010241027, 10.212288533220807) | \n", "(-12.044312010241027,) | \n", "(10.212288533220807,) | \n", "(0.00980392156862745, 0.0, 0.00666011085285177... | \n", "
ATTGGTCTAGTTCG_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-7.030158280633503, 8.796354089778507) | \n", "(-7.030158280633503,) | \n", "(8.796354089778507,) | \n", "(0.008525149190110827, 0.0, 0.0050584063412599... | \n", "
CAAGCTGATAGCCA_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-10.665383078424052, 9.747860339415233) | \n", "(-10.665383078424052,) | \n", "(9.747860339415233,) | \n", "(0.0, 0.0, 0.005326598724596222, 0.00679634403... | \n", "
CACTTATGAGGTTC_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-8.521131864483003, 8.709265916027528) | \n", "(-8.521131864483003,) | \n", "(8.709265916027528,) | \n", "(0.0, 0.0, 0.004171881518564873, 0.00534137957... | \n", "
GAACGGGACCTGTC_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-9.472612023093651, 7.224376769081281) | \n", "(-9.472612023093651,) | \n", "(7.224376769081281,) | \n", "(0.0, 0.0, 0.005460694916264378, 0.00715764393... | \n", "
GACTCCTGTATCGG_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-10.375473572514034, 7.936497570027164) | \n", "(-10.375473572514034,) | \n", "(7.936497570027164,) | \n", "(0.0, 0.0, 0.006630311699147744, 0.00869072728... | \n", "
GGTTTACTTGACCA_3 | \n", "4 | \n", "Fibroblast 5 (fibroblasts) | \n", "(4,) | \n", "(-9.295469167269326, 9.5103727114457) | \n", "(-9.295469167269326,) | \n", "(9.5103727114457,) | \n", "(0.007246376811594203, 0.0, 0.0043208772870850... | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
GGGTCTGGTCCGAAGA_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(9.427422568970837, 14.663131381946132) | \n", "(9.427422568970837,) | \n", "(14.663131381946132,) | \n", "(0.0, 0.0, 0.003069312831515585, 0.00374970705... | \n", "
GTAACGTTCCTCTAGC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(20.49311597757284, 18.437047303448296) | \n", "(20.49311597757284,) | \n", "(18.437047303448296,) | \n", "(0.0, 0.0, 0.0050509565528339, 0.0051363174751... | \n", "
GTCACAAGTTCCTCCA_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(19.51768984376519, 17.455328489541145) | \n", "(19.51768984376519,) | \n", "(17.455328489541145,) | \n", "(0.0, 0.0, 0.006458966565349544, 0.00722599796... | \n", "
GTCGTAAAGTCTCCTC_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(2.371708652265448, 7.458358341363119) | \n", "(2.371708652265448,) | \n", "(7.458358341363119,) | \n", "(0.0006393861892583121, 0.0007606490872210953,... | \n", "
GTCGTAACACTTAAGC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(20.152451420275312, 17.744118929400447) | \n", "(20.152451420275312,) | \n", "(17.744118929400447,) | \n", "(0.0, 0.0, 0.0072933428690625185, 0.0078900085... | \n", "
GTCGTAATCACTCCTG_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(1.2179563306775463, 6.081412783475383) | \n", "(1.2179563306775463,) | \n", "(6.081412783475383,) | \n", "(0.0, 0.0, 0.008403361344537815, 0.00996992422... | \n", "
GTTACAGCAATCCGAT_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(5.117152781369393, 2.7738210769009903) | \n", "(5.117152781369393,) | \n", "(2.7738210769009903,) | \n", "(0.0, 0.0, 0.0051105548602419695, 0.0058882118... | \n", "
TAAGCGTGTTTGACTG_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(6.378363156947139, 13.686908246452042) | \n", "(6.378363156947139,) | \n", "(13.686908246452042,) | \n", "(0.0, 0.0, 0.00740508969545265, 0.008163424732... | \n", "
TACGGGCTCTTCGGTC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(20.72524939866307, 15.482568141908592) | \n", "(20.72524939866307,) | \n", "(15.482568141908592,) | \n", "(0.0, 0.0, 0.008127719172775494, 0.00811460042... | \n", "
TACTCATAGGTGTTAA_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(4.294921950028606, 28.566866280068847) | \n", "(4.294921950028606,) | \n", "(28.566866280068847,) | \n", "(0.0, 0.0, 0.00883544907324632, 0.009471916256... | \n", "
TAGTGGTAGAAGGCCT_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(1.3418554924019888, 6.945583935946567) | \n", "(1.3418554924019888,) | \n", "(6.945583935946567,) | \n", "(0.0013853367433930093, 0.0, 0.005550092377376... | \n", "
TCAACGATCTCAAACG_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(17.903432064658855, 11.095363988039779) | \n", "(17.903432064658855,) | \n", "(11.095363988039779,) | \n", "(0.0, 0.0, 0.009274986590380833, 0.00802671666... | \n", "
TCACGAAGTTTGTTTC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(11.947581449870958, 28.120022103238796) | \n", "(11.947581449870958,) | \n", "(28.120022103238796,) | \n", "(0.00021312872975277067, 0.0, 0.00803087192323... | \n", "
TCAGCAAAGCGATCCC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(9.39590567953515, 32.47870114453407) | \n", "(9.39590567953515,) | \n", "(32.47870114453407,) | \n", "(0.0, 0.0, 0.009021693783896537, 0.00886649480... | \n", "
TCCACACTCGTGGGAA_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(7.975860302077773, 11.461310823257106) | \n", "(7.975860302077773,) | \n", "(11.461310823257106,) | \n", "(0.0, 0.0, 0.007717980809345015, 0.00987227560... | \n", "
TCCACACTCTGGGCCA_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(6.0033448579222854, 11.598902297910067) | \n", "(6.0033448579222854,) | \n", "(11.598902297910067,) | \n", "(0.014705882352941176, 0.009381338742393509, 0... | \n", "
TCGGTAAAGAAACCGC_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(6.267839831328621, 6.522741117394964) | \n", "(6.267839831328621,) | \n", "(6.522741117394964,) | \n", "(0.0, 0.0, 0.007211395196376423, 0.00932544332... | \n", "
TCTCATACAAGTACCT_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(16.85234635277008, 17.597543983375648) | \n", "(16.85234635277008,) | \n", "(17.597543983375648,) | \n", "(0.0, 0.0, 0.004238929614398951, 0.00555620654... | \n", "
TCTGAGAAGACACTAA_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(20.60888063822514, 14.824445025317731) | \n", "(20.60888063822514,) | \n", "(14.824445025317731,) | \n", "(0.0, 0.0, 0.006868704928780022, 0.00881767049... | \n", "
TGCCAAAGTAGCTCCG_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(18.49965519582527, 13.049893525143053) | \n", "(18.49965519582527,) | \n", "(13.049893525143053,) | \n", "(0.0, 0.0, 0.007062399427856249, 0.00909108663... | \n", "
TGGCGCACAGGCGATA_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(7.602470456900356, 15.927743194797266) | \n", "(7.602470456900356,) | \n", "(15.927743194797266,) | \n", "(0.0, 0.0, 0.006019429048215031, 0.00742129521... | \n", "
TGGGCGTCAAGTCTGT_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(2.376360604095039, 27.048086098902484) | \n", "(2.376360604095039,) | \n", "(27.048086098902484,) | \n", "(0.0, 0.0, 0.009111091245008642, 0.00859307866... | \n", "
TTCGAAGAGAGAGCTC_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(4.030406798999572, 22.556916318702186) | \n", "(4.030406798999572,) | \n", "(22.556916318702186,) | \n", "(0.0, 0.0, 0.004253829191250969, 0.00555620654... | \n", "
TTGCCGTTCTGATTCT_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(7.975182708555852, 12.410496675995697) | \n", "(7.975182708555852,) | \n", "(12.410496675995697,) | \n", "(0.003090366581415175, 0.0, 0.0028979676977173... | \n", "
TTGTAGGGTTGGAGGT_23 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(1.37545433482995, 28.047303130105806) | \n", "(1.37545433482995,) | \n", "(28.047303130105806,) | \n", "(0.0, 0.0, 0.007636033136658919, 0.00787047886... | \n", "
TTTACTGTCCTCCTAG_23 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(5.07507384659054, 6.879629695838972) | \n", "(5.07507384659054,) | \n", "(6.879629695838972,) | \n", "(0.0, 0.0, 0.007278443292210501, 0.00921802984... | \n", "
CAACCTCTCATAACCG_24 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(11.946118139704941, 13.847173096455192) | \n", "(11.946118139704941,) | \n", "(13.847173096455192,) | \n", "(0.0010656436487638534, 0.0012677484787018255,... | \n", "
CTGCTGTAGTTGAGTA_24 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(5.249279975060996, 7.665258784996239) | \n", "(5.249279975060996,) | \n", "(7.665258784996239,) | \n", "(0.0, 0.0, 0.005646939626914596, 0.00632763065... | \n", "
GCATGATGTACCGTTA_24 | \n", "1 | \n", "Fibroblast 2 (fibroblasts) | \n", "(1,) | \n", "(11.269130308051462, 23.822624483496547) | \n", "(11.269130308051462,) | \n", "(23.822624483496547,) | \n", "(0.0, 0.0, 0.0052074021097800825, 0.0055952659... | \n", "
GGAAAGCTCCCACTTG_24 | \n", "2 | \n", "Fibroblast 3 (lower quality fibroblasts) | \n", "(2,) | \n", "(5.9337138056885985, 3.9638863186081275) | \n", "(5.9337138056885985,) | \n", "(3.9638863186081275,) | \n", "(0.0, 0.0, 0.008686453304726146, 0.01138582923... | \n", "
1465 rows × 7 columns
\n", "