{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/ssm-user/anaconda3/envs/scATAC/lib/python3.8/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 pandas as pd\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "import anndata\n", "from nero import Harmonia" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "demux = Harmonia.MuxOut(\"/covid/demux/merged/freemux_merged.clust1.samples.gz\")" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "dict_keys(['path', 'label', 'raw', 'muxtype', 'type', 'usefulcols', 'useful_cols_run', 'store_meta_run', 'data', 'num_drops', 'num_sng', 'num_dbl', 'num_amb', 'sngrate', 'dblrate', 'ambrate', 'sngrate_nonamb', 'dblrate_nonamb', 'inds'])" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "demux.__dict__.keys()" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | NUM.SNPS | \n", "NUM.READS | \n", "DROPLET.TYPE | \n", "BEST.GUESS | \n", "
---|---|---|---|---|
BARCODE | \n", "\n", " | \n", " | \n", " | \n", " |
GCGCGATCACAGGTTT-0 | \n", "2490 | \n", "7241 | \n", "SNG | \n", "3 | \n", "
CTTACCGCACGACTCG-0 | \n", "1354 | \n", "2808 | \n", "SNG | \n", "10 | \n", "
GCTGGGTGTCTCACCT-0 | \n", "1200 | \n", "2222 | \n", "SNG | \n", "17 | \n", "
CACACCTTCTTGACGA-0 | \n", "1529 | \n", "3593 | \n", "SNG | \n", "4 | \n", "
CAGCAGCAGACCGGAT-0 | \n", "462 | \n", "782 | \n", "SNG | \n", "16 | \n", "