{ "cells": [ { "cell_type": "markdown", "id": "59ccacc6-e526-4083-b099-9d4da6bca9d1", "metadata": {}, "source": [ "# Assign B cell annotations\n", "\n", "To assemble our annotations, we'll read our clustered B cell data and assign our expert annotations to those clusters. We'll then inspect the annotations in our UMAP projections, and output final labels for these cells.\n", "\n", "For B cells, we have two groups of cells to label - Most of the B cells were assigned labels at one resolution, and the non-effector memory B cells were assigned labels after additional, iterative clustering. So, we'll load both of these sets, remove the memory cells from the rest of the B cells, assign identities based on clusters in each, and finally concatenate all of the cell barcodes." ] }, { "cell_type": "code", "execution_count": 1, "id": "f4d9acd5-48fd-4101-8cea-3032d790c4bd", "metadata": {}, "outputs": [], "source": [ "import warnings\n", "warnings.simplefilter(action='ignore', category=FutureWarning)\n", "warnings.simplefilter(action='ignore', category=RuntimeWarning)\n", "\n", "from datetime import date\n", "import hisepy\n", "import os\n", "import pandas as pd\n", "import scanpy as sc" ] }, { "cell_type": "markdown", "id": "09a6204b-ccf7-4d88-a647-730c6f50c6dd", "metadata": {}, "source": [ "### Helper function\n", "\n", "This function makes it easy to pull csv files stored in HISE as a pandas data.frame" ] }, { "cell_type": "code", "execution_count": 2, "id": "2ea424e4-8b0e-4b25-8f39-80f762c67c0e", "metadata": {}, "outputs": [], "source": [ "def read_csv_uuid(csv_uuid):\n", " csv_path = '/home/jupyter/cache/{u}'.format(u = csv_uuid)\n", " if not os.path.isdir(csv_path):\n", " hise_res = hisepy.reader.cache_files([csv_uuid])\n", " csv_filename = os.listdir(csv_path)[0]\n", " csv_file = '{p}/{f}'.format(p = csv_path, f = csv_filename)\n", " df = pd.read_csv(csv_file, index_col = 0)\n", " return df" ] }, { "cell_type": "markdown", "id": "f6671b2b-d1d2-4de6-9e0d-7e1ff6927274", "metadata": {}, "source": [ "## Read subclustering results from HISE" ] }, { "cell_type": "code", "execution_count": 3, "id": "e8f0f269-8be7-4341-b96c-aa31f611adf4", "metadata": {}, "outputs": [], "source": [ "cell_class = 'b-cells'" ] }, { "cell_type": "code", "execution_count": 4, "id": "eff64d51-76cf-4133-9729-8e302e1e749f", "metadata": {}, "outputs": [], "source": [ "h5ad_uuid = '99f83994-26ee-49af-a882-c1f2558daed2'\n", "h5ad_path = '/home/jupyter/cache/{u}'.format(u = h5ad_uuid)" ] }, { "cell_type": "code", "execution_count": 5, "id": "a591db13-2b72-4c61-ac29-16ae1bcceb69", "metadata": {}, "outputs": [], "source": [ "if not os.path.isdir(h5ad_path):\n", " hise_res = hisepy.reader.cache_files([h5ad_uuid])" ] }, { "cell_type": "code", "execution_count": 6, "id": "ce6d003c-8783-4fb2-be2d-8306ea9865fb", "metadata": {}, "outputs": [], "source": [ "h5ad_filename = os.listdir(h5ad_path)[0]\n", "h5ad_file = '{p}/{f}'.format(p = h5ad_path, f = h5ad_filename)" ] }, { "cell_type": "code", "execution_count": 7, "id": "c0faf3a9-ca76-4a6e-99e1-3f1e082eddc1", "metadata": { "tags": [] }, "outputs": [], "source": [ "adata = sc.read_h5ad(h5ad_file)" ] }, { "cell_type": "code", "execution_count": 8, "id": "d8ede5bc-8f6d-4d4d-bd39-836b73697cd4", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(177994, 1209)" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "adata.shape" ] }, { "cell_type": "markdown", "id": "abfb5218-ad6d-48b3-91e9-3734ad1c2d0f", "metadata": {}, "source": [ "## Read memory cell subclustering results from HISE" ] }, { "cell_type": "code", "execution_count": 9, "id": "2af9df2a-b5a7-4f09-bb8b-f2d62d49120f", "metadata": {}, "outputs": [], "source": [ "mem_uuid = '51838754-b378-4f13-b447-82511bcd0a66'\n", "mem_path = '/home/jupyter/cache/{u}'.format(u = mem_uuid)" ] }, { "cell_type": "code", "execution_count": 10, "id": "796a73b1-b43b-4a79-92a0-aefec7a65c07", "metadata": {}, "outputs": [], "source": [ "if not os.path.isdir(mem_path):\n", " hise_res = hisepy.reader.cache_files([mem_path])" ] }, { "cell_type": "code", "execution_count": 11, "id": "1ba4abe3-8f12-4020-83e6-5033cde8972d", "metadata": {}, "outputs": [], "source": [ "mem_filename = os.listdir(mem_path)[0]\n", "mem_file = '{p}/{f}'.format(p = mem_path, f = mem_filename)" ] }, { "cell_type": "code", "execution_count": 12, "id": "bbaad063-dfb3-4fdb-9912-ece12c95e0c8", "metadata": { "tags": [] }, "outputs": [], "source": [ "mem_adata = sc.read_h5ad(mem_file)" ] }, { "cell_type": "code", "execution_count": 13, "id": "60385046-a779-45c0-abe2-93d987779a22", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "AnnData object with n_obs × n_vars = 47886 × 2110\n", " obs: 'barcodes', 'batch_id', 'cell_name', 'cell_uuid', 'chip_id', 'hto_barcode', 'hto_category', 'n_genes', 'n_mito_umis', 'n_reads', 'n_umis', 'original_barcodes', 'pbmc_sample_id', 'pool_id', 'well_id', 'sample.sampleKitGuid', 'cohort.cohortGuid', 'subject.subjectGuid', 'subject.biologicalSex', 'subject.race', 'subject.ethnicity', 'subject.birthYear', 'sample.visitName', 'sample.drawDate', 'file.id', 'subject.cmv', 'subject.bmi', 'celltypist.low', 'seurat.l1', 'seurat.l1.score', 'seurat.l2', 'seurat.l2.score', 'seurat.l2.5', 'seurat.l2.5.score', 'seurat.l3', 'seurat.l3.score', 'predicted_doublet', 'doublet_score', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mito', 'log1p_total_counts_mito', 'pct_counts_mito', 'leiden', 'leiden_resolution_1', 'leiden_resolution_1.5', 'leiden_resolution_2', 'ms_leiden_2', 'umap_1', 'umap_2', 'ms_leiden_2.5'\n", " var: 'mito', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'\n", " uns: 'celltypist.low_colors', 'hvg', 'leiden', 'leiden_colors', 'leiden_resolution_2_colors', 'log1p', 'ms_leiden_2_colors', 'neighbors', 'pca', 'seurat.l2.5_colors', 'umap'\n", " obsm: 'X_pca', 'X_pca_harmony', 'X_umap'\n", " varm: 'PCs'\n", " obsp: 'connectivities', 'distances'" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mem_adata" ] }, { "cell_type": "markdown", "id": "a49f1787-9611-4815-b7d9-600aeaac1c66", "metadata": {}, "source": [ "## Subset non-memory cells" ] }, { "cell_type": "code", "execution_count": 14, "id": "3cfcd6c0-b0e1-4793-94a7-95c666fa8a43", "metadata": {}, "outputs": [], "source": [ "drop_lgl = [not x for x in adata.obs['barcodes'].isin(mem_adata.obs['barcodes'])]" ] }, { "cell_type": "code", "execution_count": 15, "id": "989be1d6-e5a1-4708-baa6-8bc7e037273a", "metadata": {}, "outputs": [], "source": [ "nonmem_adata = adata[drop_lgl].copy()" ] }, { "cell_type": "code", "execution_count": 16, "id": "02b6b24d-b55e-4d3e-96bc-58d7c34922d9", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(130108, 1209)" ] }, "execution_count": 16, "metadata": {}, "output_type": "execute_result" } ], "source": [ "nonmem_adata.shape" ] }, { "cell_type": "markdown", "id": "5de43569-58d6-4ede-86db-591924258ba3", "metadata": {}, "source": [ "## Read non-memory annotations" ] }, { "cell_type": "code", "execution_count": 17, "id": "7535c90a-679e-4aa0-be1c-157ad2278ab6", "metadata": {}, "outputs": [], "source": [ "anno_uuid = 'aed5e5f4-1166-48c1-ad84-c92aee8edcf8'" ] }, { "cell_type": "code", "execution_count": 18, "id": "4203ecf4-2031-4469-ab46-c76a9240ce2f", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "downloading fileID: aed5e5f4-1166-48c1-ad84-c92aee8edcf8\n", "Files have been successfully downloaded!\n" ] } ], "source": [ "anno = read_csv_uuid(anno_uuid)" ] }, { "cell_type": "markdown", "id": "72100724-3c7e-42bb-b6df-73423656bfdc", "metadata": {}, "source": [ "## Assign non-memory labels" ] }, { "cell_type": "code", "execution_count": 19, "id": "96621b7d-911c-43cb-a041-845179af06cc", "metadata": {}, "outputs": [], "source": [ "join_col = 'ms_leiden_2'" ] }, { "cell_type": "code", "execution_count": 20, "id": "fcf7022e-9287-416d-bd52-d8d6017b492a", "metadata": {}, "outputs": [], "source": [ "anno[join_col] = anno[join_col].astype('string').astype('category')" ] }, { "cell_type": "code", "execution_count": 21, "id": "56f1fdd5-9165-464f-ad3d-7bdc69056471", "metadata": {}, "outputs": [], "source": [ "obs = nonmem_adata.obs" ] }, { "cell_type": "code", "execution_count": 22, "id": "480f6829-11b6-4552-abfb-462486d411bf", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "130108" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sum(obs[join_col].isin(anno[join_col]))" ] }, { "cell_type": "code", "execution_count": 23, "id": "591ea3f3-9c56-4c8a-961f-a985717a8ebf", "metadata": {}, "outputs": [], "source": [ "nonmem_anno = obs.merge(anno, how = 'left', on = join_col)" ] }, { "cell_type": "code", "execution_count": 24, "id": "4ae89c90-9f67-41d4-b7fb-c9b7a236a463", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | barcodes | \n", "batch_id | \n", "cell_name | \n", "cell_uuid | \n", "chip_id | \n", "hto_barcode | \n", "hto_category | \n", "n_genes | \n", "n_mito_umis | \n", "n_reads | \n", "... | \n", "log1p_total_counts_mito | \n", "pct_counts_mito | \n", "leiden | \n", "leiden_resolution_1 | \n", "leiden_resolution_1.5 | \n", "leiden_resolution_2 | \n", "ms_leiden_2 | \n", "AIFI_L3 | \n", "AIFI_L1 | \n", "AIFI_L2 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001 | \n", "bestial_fireless_rottweiler | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "904 | \n", "58 | \n", "10269 | \n", "... | \n", "4.077537 | \n", "1.968103 | \n", "7 | \n", "7 | \n", "14 | \n", "18 | \n", "21 | \n", "T_B doublet | \n", "T_B doublet | \n", "T_B doublet | \n", "
1 | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001 | \n", "stressed_wishful_flea | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1085 | \n", "71 | \n", "12422 | \n", "... | \n", "4.276666 | \n", "1.978267 | \n", "7 | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "Core naive B cell | \n", "B cell | \n", "Naive B cell | \n", "
2 | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001 | \n", "silicone_nonsolar_snowgeese | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1152 | \n", "198 | \n", "11355 | \n", "... | \n", "5.293305 | \n", "5.899881 | \n", "10 | \n", "5 | \n", "9 | \n", "11 | \n", "11 | \n", "CD27+ effector B cell | \n", "B cell | \n", "Effector B cell | \n", "
3 | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001 | \n", "luxuriant_overrated_gypsymoth | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1769 | \n", "245 | \n", "18105 | \n", "... | \n", "5.505332 | \n", "4.552211 | \n", "7 | \n", "4 | \n", "3 | \n", "6 | \n", "1 | \n", "Transitional B cell | \n", "B cell | \n", "Transitional B cell | \n", "
4 | \n", "cf74ae2c48b611ea8957bafe6d70929e | \n", "B001 | \n", "real_bighearted_kitty | \n", "cf74ae2c48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "692 | \n", "83 | \n", "5468 | \n", "... | \n", "4.430817 | \n", "4.976019 | \n", "7 | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "Core naive B cell | \n", "B cell | \n", "Naive B cell | \n", "
5 rows × 57 columns
\n", "\n", " | barcodes | \n", "batch_id | \n", "cell_name | \n", "cell_uuid | \n", "chip_id | \n", "hto_barcode | \n", "hto_category | \n", "n_genes | \n", "n_mito_umis | \n", "n_reads | \n", "... | \n", "leiden_resolution_1 | \n", "leiden_resolution_1.5 | \n", "leiden_resolution_2 | \n", "ms_leiden_2 | \n", "umap_1 | \n", "umap_2 | \n", "ms_leiden_2.5 | \n", "AIFI_L3 | \n", "AIFI_L1 | \n", "AIFI_L2 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001 | \n", "patterny_untalented_halcyon | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "928 | \n", "66 | \n", "7856 | \n", "... | \n", "2 | \n", "4 | \n", "2 | \n", "2 | \n", "NaN | \n", "NaN | \n", "8 | \n", "Core memory B cell | \n", "B cell | \n", "Memory B cell | \n", "
1 | \n", "cf78473048b611ea8957bafe6d70929e | \n", "B001 | \n", "burly_backward_tuatara | \n", "cf78473048b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1372 | \n", "338 | \n", "17586 | \n", "... | \n", "3 | \n", "6 | \n", "13 | \n", "13 | \n", "NaN | \n", "NaN | \n", "5 | \n", "Core memory B cell | \n", "B cell | \n", "Memory B cell | \n", "
2 | \n", "cf79279a48b611ea8957bafe6d70929e | \n", "B001 | \n", "illadvised_applicable_annelid | \n", "cf79279a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "757 | \n", "207 | \n", "8651 | \n", "... | \n", "3 | \n", "7 | \n", "10 | \n", "13 | \n", "NaN | \n", "NaN | \n", "8 | \n", "Core memory B cell | \n", "B cell | \n", "Memory B cell | \n", "
3 | \n", "cf80e44e48b611ea8957bafe6d70929e | \n", "B001 | \n", "frousy_vapourific_oropendola | \n", "cf80e44e48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "776 | \n", "70 | \n", "5600 | \n", "... | \n", "2 | \n", "4 | \n", "2 | \n", "2 | \n", "NaN | \n", "NaN | \n", "8 | \n", "Core memory B cell | \n", "B cell | \n", "Memory B cell | \n", "
4 | \n", "cf81a58c48b611ea8957bafe6d70929e | \n", "B001 | \n", "minor_clerkish_hartebeest | \n", "cf81a58c48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1244 | \n", "151 | \n", "10561 | \n", "... | \n", "2 | \n", "5 | \n", "4 | \n", "2 | \n", "NaN | \n", "NaN | \n", "9 | \n", "Early memory B cell | \n", "B cell | \n", "Memory B cell | \n", "
5 rows × 60 columns
\n", "\n", " | barcodes | \n", "batch_id | \n", "cell_name | \n", "cell_uuid | \n", "chip_id | \n", "hto_barcode | \n", "hto_category | \n", "n_genes | \n", "n_mito_umis | \n", "n_reads | \n", "... | \n", "log1p_total_counts_mito | \n", "pct_counts_mito | \n", "leiden | \n", "leiden_resolution_1 | \n", "leiden_resolution_1.5 | \n", "leiden_resolution_2 | \n", "ms_leiden_2 | \n", "AIFI_L1 | \n", "AIFI_L2 | \n", "AIFI_L3 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
barcodes | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
cf720af048b611ea8957bafe6d70929e | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001 | \n", "patterny_untalented_halcyon | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "928 | \n", "66 | \n", "7856 | \n", "... | \n", "4.204693 | \n", "2.798982 | \n", "10 | \n", "2 | \n", "4 | \n", "2 | \n", "2 | \n", "B cell | \n", "Memory B cell | \n", "Core memory B cell | \n", "
cf72a14a48b611ea8957bafe6d70929e | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001 | \n", "bestial_fireless_rottweiler | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "904 | \n", "58 | \n", "10269 | \n", "... | \n", "4.077537 | \n", "1.968103 | \n", "7 | \n", "7 | \n", "14 | \n", "18 | \n", "21 | \n", "T_B doublet | \n", "T_B doublet | \n", "T_B doublet | \n", "
cf73500e48b611ea8957bafe6d70929e | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001 | \n", "stressed_wishful_flea | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1085 | \n", "71 | \n", "12422 | \n", "... | \n", "4.276666 | \n", "1.978267 | \n", "7 | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "B cell | \n", "Naive B cell | \n", "Core naive B cell | \n", "
cf73694a48b611ea8957bafe6d70929e | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001 | \n", "silicone_nonsolar_snowgeese | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1152 | \n", "198 | \n", "11355 | \n", "... | \n", "5.293305 | \n", "5.899881 | \n", "10 | \n", "5 | \n", "9 | \n", "11 | \n", "11 | \n", "B cell | \n", "Effector B cell | \n", "CD27+ effector B cell | \n", "
cf73fbee48b611ea8957bafe6d70929e | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001 | \n", "luxuriant_overrated_gypsymoth | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1769 | \n", "245 | \n", "18105 | \n", "... | \n", "5.505332 | \n", "4.552211 | \n", "7 | \n", "4 | \n", "3 | \n", "6 | \n", "1 | \n", "B cell | \n", "Transitional B cell | \n", "Transitional B cell | \n", "
5 rows × 57 columns
\n", "\n", " | barcodes | \n", "batch_id | \n", "cell_name | \n", "cell_uuid | \n", "chip_id | \n", "hto_barcode | \n", "hto_category | \n", "n_genes | \n", "n_mito_umis | \n", "n_reads | \n", "... | \n", "leiden | \n", "leiden_resolution_1 | \n", "leiden_resolution_1.5 | \n", "leiden_resolution_2 | \n", "ms_leiden_2 | \n", "AIFI_L1 | \n", "AIFI_L2 | \n", "AIFI_L3 | \n", "umap_1 | \n", "umap_2 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001 | \n", "patterny_untalented_halcyon | \n", "cf720af048b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "928 | \n", "66 | \n", "7856 | \n", "... | \n", "10 | \n", "2 | \n", "4 | \n", "2 | \n", "2 | \n", "B cell | \n", "Memory B cell | \n", "Core memory B cell | \n", "1.259842 | \n", "-1.832500 | \n", "
1 | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001 | \n", "bestial_fireless_rottweiler | \n", "cf72a14a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "904 | \n", "58 | \n", "10269 | \n", "... | \n", "7 | \n", "7 | \n", "14 | \n", "18 | \n", "21 | \n", "T_B doublet | \n", "T_B doublet | \n", "T_B doublet | \n", "1.463564 | \n", "11.663149 | \n", "
2 | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001 | \n", "stressed_wishful_flea | \n", "cf73500e48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1085 | \n", "71 | \n", "12422 | \n", "... | \n", "7 | \n", "1 | \n", "1 | \n", "0 | \n", "0 | \n", "B cell | \n", "Naive B cell | \n", "Core naive B cell | \n", "-2.856547 | \n", "-0.907700 | \n", "
3 | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001 | \n", "silicone_nonsolar_snowgeese | \n", "cf73694a48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1152 | \n", "198 | \n", "11355 | \n", "... | \n", "10 | \n", "5 | \n", "9 | \n", "11 | \n", "11 | \n", "B cell | \n", "Effector B cell | \n", "CD27+ effector B cell | \n", "3.092754 | \n", "-1.697405 | \n", "
4 | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001 | \n", "luxuriant_overrated_gypsymoth | \n", "cf73fbee48b611ea8957bafe6d70929e | \n", "B001-P1C1 | \n", "TGATGGCCTATTGGG | \n", "singlet | \n", "1769 | \n", "245 | \n", "18105 | \n", "... | \n", "7 | \n", "4 | \n", "3 | \n", "6 | \n", "1 | \n", "B cell | \n", "Transitional B cell | \n", "Transitional B cell | \n", "-3.169807 | \n", "2.543742 | \n", "
5 rows × 59 columns
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