{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "cc9d1212", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "import pandas as pd\n", "from scipy import stats, sparse\n", "import bottleneck\n", "from scipy.stats import mannwhitneyu" ] }, { "cell_type": "code", "execution_count": 212, "id": "33073b80", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "import pandas as pd\n", "from scipy import stats, sparse\n", "import bottleneck\n", "def run_egad(go, nw, **kwargs):\n", " \"\"\"EGAD running function\n", " \n", " Wrapper to lower level functions for EGAD\n", "\n", " EGAD measures modularity of gene lists in co-expression networks. \n", "\n", " This was translated from the MATLAB version, which does tiled Cross Validation\n", " \n", " The useful kwargs are:\n", " int - nFold : Number of CV folds to do, default is 3, \n", " int - {min,max}_count : limits for number of terms in each gene list, these are exclusive values\n", "\n", "\n", " Arguments:\n", " go {pd.DataFrame} -- dataframe of genes x terms of values [0,1], where 1 is included in gene lists\n", " nw {pd.DataFrame} -- dataframe of co-expression network, genes x genes\n", " **kwargs \n", " \n", " Returns:\n", " pd.DataFrame -- dataframe of terms x metrics where the metrics are \n", " ['AUC', 'AVG_NODE_DEGREE', 'DEGREE_NULL_AUC', 'P_Value']\n", " \"\"\"\n", " assert nw.shape[0] == nw.shape[1] , 'Network is not square'\n", " #print(nw.index)\n", " #nw.columns = nw.columns.astype(int)\n", " #print(nw.columns.astype(int))\n", " assert np.all(nw.index == nw.columns) , 'Network index and columns are not in the same order'\n", "\n", " #nw_mask = nw.isna().sum(axis=1) != nw.shape[1]\n", " #nw = nw.loc[nw_mask, nw_mask].astype('float')\n", " #np.fill_diagonal(nw.values, 1)\n", " return _runNV(go, nw, **kwargs)\n", "\n", "def _runNV(go, nw, nFold=3, min_count=10, max_count=1000000):\n", "\n", " #Make sure genes are same in go and nw\n", " #go.index = go.index.map(str) \n", " #nw.index = nw.index.map(str)\n", " #nw.index = nw.index.str.replace('_', '')\n", " #go.index = go.index.str.replace('_', '')\n", " #print (nw)\n", " genes_intersect = go.index.intersection(nw.index)\n", "\n", "\n", " #print (genes_intersect)\n", " go = go.loc[genes_intersect, :]\n", " nw = nw.loc[genes_intersect, genes_intersect]\n", " #print (go)\n", " print (nw.shape)\n", " print (go.shape)\n", " sparsity = 1.0 - np.count_nonzero(go) / go.size\n", " print (sparsity)\n", " sparsity = 1.0 - np.count_nonzero(nw) / nw.size\n", " print (sparsity)\n", " #print(nw\n", " #print(go\n", " nw_mask = nw.isna().sum(axis=1) != nw.shape[1]\n", " nw = nw.loc[nw_mask, nw_mask].astype('float')\n", " np.fill_diagonal(nw.values, 1)\n", " #Make sure there aren't duplicates\n", " duplicates = nw.index.duplicated(keep='first')\n", " nw = nw.loc[~duplicates, ~duplicates]\n", "\n", " go = go.loc[:, (go.sum(axis=0) > min_count) & (go.sum(axis=0) < max_count)]\n", " go = go.loc[~go.index.duplicated(keep='first'), :]\n", " #print(go)\n", "\n", " roc = _new_egad(go.values, nw.values, nFold)\n", "\n", " col_names = ['AUC', 'AVG_NODE_DEGREE', 'DEGREE_NULL_AUC', 'P_Value']\n", " #Put output in dataframe\n", " return pd.DataFrame(dict(zip(col_names, roc)), index=go.columns), go\n", "\n", "def _new_egad(go, nw, nFold):\n", "\n", " #Build Cross validated Positive\n", " x, y = np.where(go)\n", " #print(x, y)\n", " cvgo = {}\n", " for i in np.arange(nFold):\n", " a = x[i::nFold]\n", " #print(a)\n", " b = y[i::nFold]\n", " dat = np.ones_like(a)\n", " mask = sparse.coo_matrix((dat, (a, b)), shape=go.shape)\n", " cvgo[i] = go - mask.toarray()\n", "\n", " CVgo = np.concatenate(list(cvgo.values()), axis=1)\n", " #print(CVgo)\n", "\n", " sumin = np.matmul(nw.T, CVgo)\n", "\n", " degree = np.sum(nw, axis=0)\n", " #print(degree)\n", " #print(degree[:, None])\n", "\n", " predicts = sumin / degree[:, None]\n", " #print(predicts)\n", "\n", " np.place(predicts, CVgo > 0, np.nan)\n", "\n", " #print(predicts)\n", "\n", " #Calculate ranks of positives\n", " rank_abs = lambda x: stats.rankdata(np.abs(x))\n", " predicts2 = np.apply_along_axis(rank_abs, 0, predicts)\n", " #print(predicts2)\n", "\n", " #Masking Nans that were ranked (how tiedrank works in matlab)\n", " predicts2[np.isnan(predicts)] = np.nan\n", " #print(predicts2)\n", "\n", " filtering = np.tile(go, nFold)\n", " #print(filtering)\n", "\n", " #negatives :filtering == 0\n", " #Sets Ranks of negatives to 0\n", " np.place(predicts2, filtering == 0, 0)\n", "\n", " #Sum of ranks for each prediction\n", " p = bottleneck.nansum(predicts2, axis=0)\n", " n_p = np.sum(filtering, axis=0) - np.sum(CVgo, axis=0)\n", "\n", " #Number of negatives\n", " #Number of GO terms - number of postiive\n", " n_n = filtering.shape[0] - np.sum(filtering, axis=0)\n", "\n", " roc = (p / n_p - (n_p + 1) / 2) / n_n\n", " U = roc * n_p * n_n\n", " Z = (np.abs(U - (n_p * n_n / 2))) / np.sqrt(n_p * n_n *\n", " (n_p + n_n + 1) / 12)\n", " roc = roc.reshape(nFold, go.shape[1])\n", " Z = Z.reshape(nFold, go.shape[1])\n", " #Stouffer Z method\n", " Z = bottleneck.nansum(Z, axis=0) / np.sqrt(nFold)\n", " #Calc ROC of Neighbor Voting\n", " roc = bottleneck.nanmean(roc, axis=0)\n", " P = stats.norm.sf(Z)\n", "\n", " #Average degree for nodes in each go term\n", " avg_degree = degree.dot(go) / np.sum(go, axis=0)\n", "\n", " #Calc null auc for degree\n", " ranks = np.tile(stats.rankdata(degree), (go.shape[1], 1)).T\n", "\n", " np.place(ranks, go == 0, 0)\n", "\n", " n_p = bottleneck.nansum(go, axis=0)\n", " nn = go.shape[0] - n_p\n", " p = bottleneck.nansum(ranks, axis=0)\n", "\n", " roc_null = (p / n_p - ((n_p + 1) / 2)) / nn\n", " #print(roc)\n", " return roc, avg_degree, roc_null, P" ] }, { "cell_type": "code", "execution_count": 3, "id": "5cd469b7", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:numexpr.utils:Note: detected 192 virtual cores but NumExpr set to maximum of 64, check \"NUMEXPR_MAX_THREADS\" environment variable.\n", "INFO:numexpr.utils:Note: NumExpr detected 192 cores but \"NUMEXPR_MAX_THREADS\" not set, so enforcing safe limit of 8.\n", "INFO:numexpr.utils:NumExpr defaulting to 8 threads.\n" ] } ], "source": [ "from hicmatrix import HiCMatrix as hm\n", "from hicmatrix.lib import MatrixFileHandler" ] }, { "cell_type": "code", "execution_count": 4, "id": "40afe2ee", "metadata": {}, "outputs": [], "source": [ "\n", "exp_file_path=f'/grid/gillis/data/lohia/hi_c_data_processing/software/CoCoCoNet/networks/human_prioAggNet.h5'\n", "\n", "jac_exp = hm.hiCMatrix(exp_file_path)\n", "all_genes = [x[3].decode() for x in jac_exp.cut_intervals]\n", "df_exp_corr = pd.DataFrame(jac_exp.matrix.toarray() , index=all_genes, columns = all_genes)" ] }, { "cell_type": "code", "execution_count": 16, "id": "5fc018d4", "metadata": {}, "outputs": [], "source": [ "df_exp_corr = pd.DataFrame(jac_exp.matrix.toarray() , index=all_genes, columns = all_genes)\n", "\n" ] }, { "cell_type": "code", "execution_count": 5, "id": "2acb83bb", "metadata": {}, "outputs": [], "source": [ "resolution_human = 10000\n", "species = \"human\"\n", "SRP_name = \"aggregates\"\n", "resolution = \"10kbp_raw\"\n", "\n", "\n", "\n", "input_path=f'/grid/gillis/data/lohia/hi_c_data_processing/data_{species}/{SRP_name}/{resolution}/max/'\n", "bins_bed = pd.read_csv(f'{input_path}/all_bins.bed', names=['chr', 'start', 'end', 'bin_id'])" ] }, { "cell_type": "code", "execution_count": 6, "id": "1d608fb3", "metadata": {}, "outputs": [], "source": [ " if species == 'human':\n", "\n", " df_cre = pd.read_csv('/grid/gillis/data/lohia/hi_c_data_processing/data_human/aggregates/li2022/GRCh38-cCREs.bed', sep='\\t', names=['chr', 'start', 'end', 't1', 't2', 't3'])\n", "\n", " else:\n", "\n", " df_cre = pd.read_csv('/grid/gillis/data/lohia/ATAC_Risa/mm10-cCREs.bed', sep='\\t', names=['chr', 'start', 'end', 't1', 't2', 't3'])\n", "\n", " df_cre['start_bin'] = df_cre['start']/resolution_human\n", " df_cre['start_bin'] = df_cre['start_bin'].astype('int')\n", " df_cre['start_bin'] = df_cre['start_bin']*resolution_human\n", " df_cre['start_bin'] = df_cre['start_bin'].astype('str')\n", " df_cre['start_bin'] = df_cre['chr'] + '_' + df_cre['start_bin']\n", " #df_cre_1kb_encode = df_cre.drop_duplicates(subset=['start_bin'])\n", " df_cre['cre'] = 1\n", " df_cre = df_cre.groupby(['start_bin'])['cre'].sum().reset_index()\n", " input_path=f'/grid/gillis/data/lohia/hi_c_data_processing/data_{species}/{SRP_name}/{resolution}/max/'\n", " bins_bed = pd.read_csv(f'{input_path}/all_bins.bed', names=['chr', 'start', 'end', 'bin_id'])\n", " bins_bed['bin_id'] = bins_bed.index\n", " bins_bed['pos'] = bins_bed['chr'] + '_' + bins_bed['start'].astype('str')\n", " df_cre_1kb_encode = df_cre.merge(bins_bed, left_on='start_bin', right_on='pos')\n", " \n", " " ] }, { "cell_type": "code", "execution_count": 8, "id": "50de8551", "metadata": {}, "outputs": [], "source": [ "from hicmatrix import HiCMatrix as hm\n", "from hicmatrix.lib import MatrixFileHandler\n", "import numpy as np\n", "import pandas as pd\n", "from scipy import stats, sparse\n", "import bottleneck\n", "from scipy.stats import mannwhitneyu\n", "import h5py\n", "import h5py\n", "import logging\n", "import numpy as np\n", "import pandas as pd\n", "from hicmatrix import HiCMatrix as hm\n", "from hicmatrix.lib import MatrixFileHandler\n", "from scipy.sparse import csr_matrix, dia_matrix, triu, tril, coo_matrix\n", "import scipy.stats as stats\n", "import os.path" ] }, { "cell_type": "code", "execution_count": 10, "id": "fa98cc26", "metadata": {}, "outputs": [], "source": [ "with h5py.File(f'/grid/gillis/data/lohia/hi_c_data_processing/data_{species}/{SRP_name}/{resolution}/max/hic_gene_gw_none_by_allbins_none_ranked_inter.h5', 'r') as hf:\n", " my_data = hf['matrix'][:]\n", " gene_list = hf['gene_list'][:]\n", " bins_bed = hf['bins_bed'][:]\n", " " ] }, { "cell_type": "code", "execution_count": 282, "id": "3a28adb6", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([ 0, 1, 2, ..., 287506, 287507, 287508])" ] }, "execution_count": 282, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bins_bed" ] }, { "cell_type": "code", "execution_count": 134, "id": "92a6801c", "metadata": {}, "outputs": [], "source": [ "my_percen = np.nanpercentile(my_data, 99, axis=1, keepdims=True)" ] }, { "cell_type": "code", "execution_count": 135, "id": "e19b89c8", "metadata": {}, "outputs": [], "source": [ "my_data_thresh = my_data > my_percen\n", "\n", "my_data_thresh = my_data_thresh.astype(int)" ] }, { "cell_type": "code", "execution_count": 136, "id": "c5566c6f", "metadata": {}, "outputs": [], "source": [ "df_gene_tp = pd.DataFrame(my_data_thresh , index=[x.decode() for x in gene_list.tolist()], columns = bins_bed.tolist())\n" ] }, { "cell_type": "code", "execution_count": 45, "id": "33857316", "metadata": {}, "outputs": [], "source": [ "df_gene_tp_all = pd.DataFrame(my_data , index=[x.decode() for x in gene_list.tolist()], columns = bins_bed.tolist())\n" ] }, { "cell_type": "code", "execution_count": 46, "id": "e7424a41", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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13158 rows × 8342 columns
\n", "\n", " | start_bin | \n", "cre | \n", "chr | \n", "start | \n", "end | \n", "bin_id | \n", "pos | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "chr10_10000 | \n", "1 | \n", "chr10 | \n", "10000 | \n", "20000 | \n", "167493 | \n", "chr10_10000 | \n", "
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2 | \n", "chr10_1000000 | \n", "1 | \n", "chr10 | \n", "1000000 | \n", "1010000 | \n", "167592 | \n", "chr10_1000000 | \n", "
3 | \n", "chr10_10000000 | \n", "6 | \n", "chr10 | \n", "10000000 | \n", "10010000 | \n", "168492 | \n", "chr10_10000000 | \n", "
4 | \n", "chr10_100000000 | \n", "16 | \n", "chr10 | \n", "100000000 | \n", "100010000 | \n", "177492 | \n", "chr10_100000000 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
213396 | \n", "chr9_99940000 | \n", "1 | \n", "chr9 | \n", "99940000 | \n", "99950000 | \n", "163646 | \n", "chr9_99940000 | \n", "
213397 | \n", "chr9_99950000 | \n", "1 | \n", "chr9 | \n", "99950000 | \n", "99960000 | \n", "163647 | \n", "chr9_99950000 | \n", "
213398 | \n", "chr9_99960000 | \n", "1 | \n", "chr9 | \n", "99960000 | \n", "99970000 | \n", "163648 | \n", "chr9_99960000 | \n", "
213399 | \n", "chr9_99970000 | \n", "2 | \n", "chr9 | \n", "99970000 | \n", "99980000 | \n", "163649 | \n", "chr9_99970000 | \n", "
213400 | \n", "chr9_99990000 | \n", "1 | \n", "chr9 | \n", "99990000 | \n", "100000000 | \n", "163651 | \n", "chr9_99990000 | \n", "
213401 rows × 7 columns
\n", "\n", " | AUC | \n", "AVG_NODE_DEGREE | \n", "DEGREE_NULL_AUC | \n", "P_Value | \n", "index | \n", "0 | \n", "
---|---|---|---|---|---|---|
0 | \n", "0.548648 | \n", "10432.251330 | \n", "0.500019 | \n", "2.071635e-02 | \n", "177492 | \n", "147 | \n", "
1 | \n", "0.593454 | \n", "10135.578246 | \n", "0.442564 | \n", "5.234711e-02 | \n", "177557 | \n", "26 | \n", "
2 | \n", "0.536454 | \n", "10060.668246 | \n", "0.407840 | \n", "2.975338e-01 | \n", "177565 | \n", "20 | \n", "
3 | \n", "0.624543 | \n", "10300.179106 | \n", "0.478141 | \n", "5.764654e-07 | \n", "177566 | \n", "127 | \n", "
4 | \n", "0.461897 | \n", "10385.444057 | \n", "0.516128 | \n", "6.432477e-02 | \n", "177580 | \n", "129 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
7876 | \n", "0.601389 | \n", "10454.027772 | \n", "0.510980 | \n", "1.831122e-08 | \n", "163474 | \n", "249 | \n", "
7877 | \n", "0.560149 | \n", "10544.321932 | \n", "0.529888 | \n", "4.074555e-03 | \n", "163477 | \n", "159 | \n", "
7878 | \n", "0.525629 | \n", "10027.908366 | \n", "0.415976 | \n", "2.571734e-01 | \n", "163557 | \n", "60 | \n", "
7879 | \n", "0.660111 | \n", "10531.933967 | \n", "0.498688 | \n", "3.683678e-03 | \n", "163562 | \n", "32 | \n", "
7880 | \n", "0.692969 | \n", "10628.637247 | \n", "0.547172 | \n", "1.431164e-17 | \n", "163634 | \n", "162 | \n", "
7881 rows × 6 columns
\n", "\n", " | AUC | \n", "AVG_NODE_DEGREE | \n", "DEGREE_NULL_AUC | \n", "P_Value | \n", "index | \n", "0 | \n", "
---|---|---|---|---|---|---|
0 | \n", "0.548648 | \n", "10432.251330 | \n", "0.500019 | \n", "2.071635e-02 | \n", "177492 | \n", "0.006726 | \n", "
1 | \n", "0.593454 | \n", "10135.578246 | \n", "0.442564 | \n", "5.234711e-02 | \n", "177557 | \n", "0.001718 | \n", "
2 | \n", "0.536454 | \n", "10060.668246 | \n", "0.407840 | \n", "2.975338e-01 | \n", "177565 | \n", "0.001666 | \n", "
3 | \n", "0.624543 | \n", "10300.179106 | \n", "0.478141 | \n", "5.764654e-07 | \n", "177566 | \n", "0.006697 | \n", "
4 | \n", "0.461897 | \n", "10385.444057 | \n", "0.516128 | \n", "6.432477e-02 | \n", "177580 | \n", "0.006302 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
7876 | \n", "0.601389 | \n", "10454.027772 | \n", "0.510980 | \n", "1.831122e-08 | \n", "163474 | \n", "0.007217 | \n", "
7877 | \n", "0.560149 | \n", "10544.321932 | \n", "0.529888 | \n", "4.074555e-03 | \n", "163477 | \n", "0.006246 | \n", "
7878 | \n", "0.525629 | \n", "10027.908366 | \n", "0.415976 | \n", "2.571734e-01 | \n", "163557 | \n", "0.003324 | \n", "
7879 | \n", "0.660111 | \n", "10531.933967 | \n", "0.498688 | \n", "3.683678e-03 | \n", "163562 | \n", "0.001810 | \n", "
7880 | \n", "0.692969 | \n", "10628.637247 | \n", "0.547172 | \n", "1.431164e-17 | \n", "163634 | \n", "0.006360 | \n", "
7881 rows × 6 columns
\n", "\n", " | index | \n", "0_x | \n", "0_y | \n", "
---|---|---|---|
0 | \n", "177492 | \n", "0.006726 | \n", "0.011172 | \n", "
1 | \n", "177557 | \n", "0.001718 | \n", "0.001976 | \n", "
2 | \n", "177565 | \n", "0.001666 | \n", "0.001520 | \n", "
3 | \n", "177566 | \n", "0.006697 | \n", "0.009652 | \n", "
4 | \n", "177580 | \n", "0.006302 | \n", "0.009804 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "
8337 | \n", "163474 | \n", "0.007217 | \n", "0.018924 | \n", "
8338 | \n", "163477 | \n", "0.006246 | \n", "0.012084 | \n", "
8339 | \n", "163557 | \n", "0.003324 | \n", "0.004560 | \n", "
8340 | \n", "163562 | \n", "0.001810 | \n", "0.002432 | \n", "
8341 | \n", "163634 | \n", "0.006360 | \n", "0.012312 | \n", "
8342 rows × 3 columns
\n", "\n", " | AUC | \n", "AVG_NODE_DEGREE | \n", "DEGREE_NULL_AUC | \n", "P_Value | \n", "index | \n", "0 | \n", "quintile | \n", "
---|---|---|---|---|---|---|---|
5 | \n", "0.616393 | \n", "10677.110581 | \n", "0.574954 | \n", "2.229388e-68 | \n", "177591 | \n", "1983 | \n", "1 | \n", "
6 | \n", "0.643438 | \n", "10423.044345 | \n", "0.506708 | \n", "6.842470e-15 | \n", "177593 | \n", "243 | \n", "5 | \n", "
7 | \n", "0.661095 | \n", "10549.253120 | \n", "0.537769 | \n", "6.572295e-78 | \n", "177598 | \n", "1153 | \n", "2 | \n", "
10 | \n", "0.592403 | \n", "10726.062502 | \n", "0.583689 | \n", "3.225288e-27 | \n", "177673 | \n", "1163 | \n", "2 | \n", "
11 | \n", "0.628581 | \n", "10568.321206 | \n", "0.543337 | \n", "1.806364e-30 | \n", "177675 | \n", "669 | \n", "3 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
7847 | \n", "0.574790 | \n", "10368.410197 | \n", "0.494411 | \n", "1.346064e-08 | \n", "162958 | \n", "466 | \n", "3 | \n", "
7848 | \n", "0.610147 | \n", "10344.599261 | \n", "0.476780 | \n", "1.047082e-13 | \n", "162961 | \n", "370 | \n", "4 | \n", "
7859 | \n", "0.590189 | \n", "10476.625638 | \n", "0.515784 | \n", "3.574001e-08 | \n", "163139 | \n", "302 | \n", "4 | \n", "
7869 | \n", "0.653807 | \n", "10353.187277 | \n", "0.491195 | \n", "2.825903e-18 | \n", "163201 | \n", "264 | \n", "5 | \n", "
7876 | \n", "0.601389 | \n", "10454.027772 | \n", "0.510980 | \n", "1.831122e-08 | \n", "163474 | \n", "249 | \n", "5 | \n", "
3517 rows × 7 columns
\n", "\n", " | index | \n", "0 | \n", "
---|---|---|
0 | \n", "177756 | \n", "291 | \n", "
1 | \n", "177925 | \n", "243 | \n", "
2 | \n", "179205 | \n", "8 | \n", "
3 | \n", "179246 | \n", "41 | \n", "
4 | \n", "180007 | \n", "46 | \n", "
... | \n", "... | \n", "... | \n", "
348 | \n", "167382 | \n", "366 | \n", "
349 | \n", "167383 | \n", "1249 | \n", "
350 | \n", "167397 | \n", "1197 | \n", "
351 | \n", "155083 | \n", "95 | \n", "
352 | \n", "157355 | \n", "70 | \n", "
353 rows × 2 columns
\n", "\n", " | AUC | \n", "AVG_NODE_DEGREE | \n", "DEGREE_NULL_AUC | \n", "P_Value | \n", "
---|---|---|---|---|
177756 | \n", "0.694618 | \n", "10500.181796 | \n", "0.509848 | \n", "1.026297e-30 | \n", "
177925 | \n", "0.631797 | \n", "10535.329907 | \n", "0.520753 | \n", "6.526691e-13 | \n", "
179246 | \n", "0.519682 | \n", "10509.999055 | \n", "0.516117 | \n", "3.201657e-01 | \n", "
180007 | \n", "0.472075 | \n", "10166.996643 | \n", "0.449793 | \n", "9.773137e-02 | \n", "
180732 | \n", "0.705574 | \n", "10649.275532 | \n", "0.552092 | \n", "2.526553e-11 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
167382 | \n", "0.854699 | \n", "10305.766939 | \n", "0.456235 | \n", "1.929063e-121 | \n", "
167383 | \n", "0.815536 | \n", "10385.243341 | \n", "0.480409 | \n", "0.000000e+00 | \n", "
167397 | \n", "0.834100 | \n", "10380.869757 | \n", "0.475889 | \n", "0.000000e+00 | \n", "
155083 | \n", "0.609623 | \n", "10369.637178 | \n", "0.486403 | \n", "9.945919e-05 | \n", "
157355 | \n", "0.522972 | \n", "10258.660888 | \n", "0.457565 | \n", "2.325480e-01 | \n", "
317 rows × 4 columns
\n", "\n", " | AUC | \n", "AVG_NODE_DEGREE | \n", "DEGREE_NULL_AUC | \n", "P_Value | \n", "
---|---|---|---|---|
177756 | \n", "0.694618 | \n", "10500.181796 | \n", "0.509848 | \n", "1.026297e-30 | \n", "
177925 | \n", "0.631797 | \n", "10535.329907 | \n", "0.520753 | \n", "6.526691e-13 | \n", "
179246 | \n", "0.519682 | \n", "10509.999055 | \n", "0.516117 | \n", "3.201657e-01 | \n", "
180007 | \n", "0.472075 | \n", "10166.996643 | \n", "0.449793 | \n", "9.773137e-02 | \n", "
180732 | \n", "0.705574 | \n", "10649.275532 | \n", "0.552092 | \n", "2.526553e-11 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
167382 | \n", "0.854699 | \n", "10305.766939 | \n", "0.456235 | \n", "1.929063e-121 | \n", "
167383 | \n", "0.815536 | \n", "10385.243341 | \n", "0.480409 | \n", "0.000000e+00 | \n", "
167397 | \n", "0.834100 | \n", "10380.869757 | \n", "0.475889 | \n", "0.000000e+00 | \n", "
155083 | \n", "0.609623 | \n", "10369.637178 | \n", "0.486403 | \n", "9.945919e-05 | \n", "
157355 | \n", "0.522972 | \n", "10258.660888 | \n", "0.457565 | \n", "2.325480e-01 | \n", "
317 rows × 4 columns
\n", "\n", " | genes | \n", "avg_rank | \n", "gene_id_exp_file | \n", "auc | \n", "cat | \n", "avg_rank_d | \n", "
---|---|---|---|---|---|---|
0 | \n", "ENSG00000223972 | \n", "0.443509 | \n", "ENSG00000223972 | \n", "0.593487 | \n", "non | \n", "0.4 | \n", "
1 | \n", "ENSG00000227232 | \n", "0.733437 | \n", "ENSG00000227232 | \n", "0.599505 | \n", "non | \n", "0.7 | \n", "
2 | \n", "ENSG00000278267 | \n", "0.548917 | \n", "ENSG00000278267 | \n", "0.593487 | \n", "non | \n", "0.5 | \n", "
3 | \n", "ENSG00000243485 | \n", "0.397697 | \n", "ENSG00000243485 | \n", "0.557661 | \n", "non | \n", "0.4 | \n", "
4 | \n", "ENSG00000284332 | \n", "0.301684 | \n", "ENSG00000284332 | \n", "0.547544 | \n", "non | \n", "0.3 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
55406 | \n", "ENSG00000100312 | \n", "0.311248 | \n", "ENSG00000100312 | \n", "0.551436 | \n", "non | \n", "0.3 | \n", "
55407 | \n", "ENSG00000254499 | \n", "0.308634 | \n", "ENSG00000254499 | \n", "0.535070 | \n", "non | \n", "0.3 | \n", "
55408 | \n", "ENSG00000213683 | \n", "0.303345 | \n", "ENSG00000213683 | \n", "0.499738 | \n", "non | \n", "0.3 | \n", "
55409 | \n", "ENSG00000184319 | \n", "0.811295 | \n", "ENSG00000184319 | \n", "0.720974 | \n", "non | \n", "0.8 | \n", "
55410 | \n", "ENSG00000079974 | \n", "0.854376 | \n", "ENSG00000079974 | \n", "0.717120 | \n", "marker | \n", "0.9 | \n", "
55411 rows × 6 columns
\n", "\n", " | genes | \n", "avg_rank | \n", "gene_id_exp_file | \n", "auc | \n", "cat | \n", "avg_rank_d | \n", "
---|---|---|---|---|---|---|
0 | \n", "ENSG00000223972 | \n", "0.443509 | \n", "ENSG00000223972 | \n", "0.593487 | \n", "non | \n", "0.4 | \n", "
1 | \n", "ENSG00000227232 | \n", "0.733437 | \n", "ENSG00000227232 | \n", "0.599505 | \n", "non | \n", "0.7 | \n", "
2 | \n", "ENSG00000278267 | \n", "0.548917 | \n", "ENSG00000278267 | \n", "0.593487 | \n", "non | \n", "0.5 | \n", "
3 | \n", "ENSG00000243485 | \n", "0.397697 | \n", "ENSG00000243485 | \n", "0.557661 | \n", "non | \n", "0.4 | \n", "
4 | \n", "ENSG00000284332 | \n", "0.301684 | \n", "ENSG00000284332 | \n", "0.547544 | \n", "non | \n", "0.3 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
55406 | \n", "ENSG00000100312 | \n", "0.311248 | \n", "ENSG00000100312 | \n", "0.551436 | \n", "non | \n", "0.3 | \n", "
55407 | \n", "ENSG00000254499 | \n", "0.308634 | \n", "ENSG00000254499 | \n", "0.535070 | \n", "non | \n", "0.3 | \n", "
55408 | \n", "ENSG00000213683 | \n", "0.303345 | \n", "ENSG00000213683 | \n", "0.499738 | \n", "non | \n", "0.3 | \n", "
55409 | \n", "ENSG00000184319 | \n", "0.811295 | \n", "ENSG00000184319 | \n", "0.720974 | \n", "non | \n", "0.8 | \n", "
55410 | \n", "ENSG00000079974 | \n", "0.854376 | \n", "ENSG00000079974 | \n", "0.717120 | \n", "marker | \n", "0.9 | \n", "
55411 rows × 6 columns
\n", "\n", " | genes | \n", "avg_rank | \n", "gene_id_exp_file | \n", "auc | \n", "cat | \n", "
---|---|---|---|---|---|
0 | \n", "ENSG00000223972 | \n", "0.443509 | \n", "ENSG00000223972 | \n", "0.593487 | \n", "non | \n", "
1 | \n", "ENSG00000227232 | \n", "0.733437 | \n", "ENSG00000227232 | \n", "0.599505 | \n", "non | \n", "
2 | \n", "ENSG00000278267 | \n", "0.548917 | \n", "ENSG00000278267 | \n", "0.593487 | \n", "non | \n", "
3 | \n", "ENSG00000243485 | \n", "0.397697 | \n", "ENSG00000243485 | \n", "0.557661 | \n", "non | \n", "
4 | \n", "ENSG00000284332 | \n", "0.301684 | \n", "ENSG00000284332 | \n", "0.547544 | \n", "non | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
55406 | \n", "ENSG00000100312 | \n", "0.311248 | \n", "ENSG00000100312 | \n", "0.551436 | \n", "non | \n", "
55407 | \n", "ENSG00000254499 | \n", "0.308634 | \n", "ENSG00000254499 | \n", "0.535070 | \n", "non | \n", "
55408 | \n", "ENSG00000213683 | \n", "0.303345 | \n", "ENSG00000213683 | \n", "0.499738 | \n", "non | \n", "
55409 | \n", "ENSG00000184319 | \n", "0.811295 | \n", "ENSG00000184319 | \n", "0.720974 | \n", "non | \n", "
55410 | \n", "ENSG00000079974 | \n", "0.854376 | \n", "ENSG00000079974 | \n", "0.717120 | \n", "marker | \n", "
55411 rows × 5 columns
\n", "\n", " | group | \n", "cell_type | \n", "rank | \n", "gene | \n", "recurrence | \n", "auroc | \n", "fold_change | \n", "fold_change_detection | \n", "expression | \n", "precision | \n", "... | \n", "H200.1025_SSv4 | \n", "H200.1023_SSv4 | \n", "H18.30.002_10Xv3 | \n", "H200.1023_10Xv3 | \n", "H18.30.001_10Xv3 | \n", "H19.30.001_10Xv3 | \n", "H19.30.001_NextGEM | \n", "H19.30.002_10Xv3 | \n", "Ensembl_gene_identifier | \n", "Symbol | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "Astro | \n", "Astro_1 | \n", "1 | \n", "DPP10-AS3 | \n", "3 | \n", "0.797253 | \n", "3.094005 | \n", "1.818261 | \n", "0.000000 | \n", "0.092445 | \n", "... | \n", "False | \n", "NaN | \n", "True | \n", "NaN | \n", "NaN | \n", "False | \n", "True | \n", "True | \n", "ENSG00000231538 | \n", "DPP10-AS3 | \n", "
1 | \n", "Astro | \n", "Astro_1 | \n", "2 | \n", "DPP10 | \n", "2 | \n", "0.893438 | \n", "3.436569 | \n", "1.204534 | \n", "4519.887362 | \n", "0.026629 | \n", "... | \n", "False | \n", "NaN | \n", "True | \n", "NaN | \n", "NaN | \n", "False | \n", "True | \n", "False | \n", "ENSG00000175497 | \n", "DPP10 | \n", "
2 | \n", "Astro | \n", "Astro_1 | \n", "3 | \n", "ID2 | \n", "1 | \n", "0.792967 | \n", "2.405181 | \n", "1.507432 | \n", "157.828504 | \n", "0.033903 | \n", "... | \n", "False | \n", "NaN | \n", "False | \n", "NaN | \n", "NaN | \n", "False | \n", "False | \n", "True | \n", "ENSG00000115738 | \n", "ID2 | \n", "
3 | \n", "Astro | \n", "Astro_1 | \n", "4 | \n", "JUNB | \n", "1 | \n", "0.723300 | \n", "1.565228 | \n", "1.783512 | \n", "0.000000 | \n", "0.074596 | \n", "... | \n", "False | \n", "NaN | \n", "False | \n", "NaN | \n", "NaN | \n", "False | \n", "False | \n", "True | \n", "ENSG00000171223 | \n", "JUNB | \n", "
4 | \n", "Astro | \n", "Astro_1 | \n", "5 | \n", "GPC6 | \n", "1 | \n", "0.693258 | \n", "1.279651 | \n", "2.200657 | \n", "27.131271 | \n", "0.053557 | \n", "... | \n", "False | \n", "NaN | \n", "False | \n", "NaN | \n", "NaN | \n", "False | \n", "True | \n", "False | \n", "ENSG00000183098 | \n", "GPC6 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
14434 | \n", "VLMC | \n", "VLMC_2 | \n", "895 | \n", "DHCR7 | \n", "0 | \n", "0.600624 | \n", "4.999688 | \n", "13.836867 | \n", "0.000000 | \n", "NaN | \n", "... | \n", "NaN | \n", "False | \n", "False | \n", "NaN | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENSG00000172893 | \n", "DHCR7 | \n", "
14435 | \n", "VLMC | \n", "VLMC_2 | \n", "909 | \n", "PGF | \n", "0 | \n", "0.599718 | \n", "3.393679 | \n", "6.606525 | \n", "0.000000 | \n", "NaN | \n", "... | \n", "NaN | \n", "False | \n", "False | \n", "NaN | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENSG00000119630 | \n", "PGF | \n", "
14436 | \n", "VLMC | \n", "VLMC_2 | \n", "910 | \n", "VAT1 | \n", "0 | \n", "0.599639 | \n", "3.673718 | \n", "7.085874 | \n", "0.000000 | \n", "NaN | \n", "... | \n", "NaN | \n", "False | \n", "False | \n", "NaN | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENSG00000108828 | \n", "VAT1 | \n", "
14437 | \n", "VLMC | \n", "VLMC_2 | \n", "920 | \n", "DCAF15 | \n", "0 | \n", "0.599207 | \n", "1.939877 | \n", "4.796181 | \n", "0.000000 | \n", "NaN | \n", "... | \n", "NaN | \n", "False | \n", "False | \n", "NaN | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENSG00000132017 | \n", "DCAF15 | \n", "
14438 | \n", "VLMC | \n", "VLMC_2 | \n", "996 | \n", "RUVBL2 | \n", "0 | \n", "0.596416 | \n", "3.699655 | \n", "7.986018 | \n", "0.000000 | \n", "NaN | \n", "... | \n", "NaN | \n", "False | \n", "False | \n", "NaN | \n", "False | \n", "False | \n", "False | \n", "False | \n", "ENSG00000183207 | \n", "RUVBL2 | \n", "
14419 rows × 24 columns
\n", "