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# Learning about the CZ CELLxGENE Census

Source: `vignettes/comp_bio_census_info.Rmd`
`comp_bio_census_info.Rmd`

This notebook showcases the Census contents and how to obtain high-level information about it. It covers the organization of data within the Census, what cell and gene metadata are available, and it provides simple demonstrations to summarize cell counts across cell metadata.

Contents

- Opening the census
- Census organization
- Cell metadata
- Gene metadata
- Census summary content tables
- Understanding Census contents beyond the summary tables

## Opening the Census

The `cellxgene.census` R package contains a convenient `open_soma()` API to open any version of the Census (`stable` by default).

    library("cellxgene.census")
    census <- open_soma()

You can learn more about the cellxgene.census methods by accessing their corresponding documentation, for example `?cellxgene.census::open_soma`.

## Census organization

The Census schema defines the structure of the Census. In short, you can think of the Census as a structured collection of items that stores different pieces of information. All of these items and the parent collection are SOMA objects of various types and can all be accessed with the TileDB-SOMA API (documentation).

The `cellxgene.census` package contains some convenient wrappers of the TileDB-SOMA API. An example of this is the function we used to open the Census: `cellxgene_census.open_soma()`.

### Main Census components

With the command above you created `census`, which is a `SOMACollection`, an R6 class providing a key-value associative map. Its `get()` method can access the two top-level collection members, `census_info` and `census_data`, each themselves instances of `SOMACollection`.

### Census summary info

- `census$get("census_info")`: A collection of data frames providing information of the census as a whole.
  - `census$get("census_info")$get("summary")`: A data frame with high-level information of this Census, e.g. build date, total cell count, etc.
  - `census$get("census_info")$get("datasets")`: A data frame with all datasets from CELLxGENE Discover used to create the Census.
  - `census$get("census_info")$get("summary_cell_counts")`: A data frame with cell counts stratified by relevant cell metadata

- ### Census data

Data for each organism is stored in independent `SOMAExperiment` objects which are a specialized form of a `SOMACollection`. Each of these store a data matrix (cell by genes), cell metadata, gene metadata, and some other useful components not covered in this notebook.

This is how the data is organized for one organism – Homo sapiens:

- `census$get("census_data")$get("homo_sapiens")$obs`: Cell metadata
- `census$get("census_data")$get("homo_sapiens")$ms$get("RNA")`: Data matrices, currently only…
- `census$get("census_data")$get("homo_sapiens")$ms$get("RNA")$X$get("raw")`: a matrix of raw counts as a `SOMASparseNDArray`
- `census$get("census_data")$get("homo_sapiens")$ms$get("RNA")$var`: Gene Metadata

## Cell metadata

You can obtain all cell metadata variables by directly querying the columns of the corresponding `SOMADataFrame`.

All of these variables can be used for querying the Census in case you want to work with specific cells.

    census$get("census_data")$get("homo_sapiens")$obs$colnames()
    #>  [1] "soma_joinid"
    #>  [2] "dataset_id"
    #>  [3] "assay"
    #>  [4] "assay_ontology_term_id"
    #>  [5] "cell_type"
    #>  [6] "cell_type_ontology_term_id"
    #>  [7] "development_stage"
    #>  [8] "development_stage_ontology_term_id"
    #>  [9] "disease"
    #> [10] "disease_ontology_term_id"
    #> [11] "donor_id"
    #> [12] "is_primary_data"
    #> [13] "observation_joinid"
    #> [14] "self_reported_ethnicity"
    #> [15] "self_reported_ethnicity_ontology_term_id"
    #> [16] "sex"
    #> [17] "sex_ontology_term_id"
    #> [18] "suspension_type"
    #> [19] "tissue"
    #> [20] "tissue_ontology_term_id"
    #> [21] "tissue_type"
    #> [22] "tissue_general"
    #> [23] "tissue_general_ontology_term_id"
    #> [24] "raw_sum"
    #> [25] "nnz"
    #> [26] "raw_mean_nnz"
    #> [27] "raw_variance_nnz"
    #> [28] "n_measured_vars"

All of these variables are defined in the CELLxGENE dataset schema except for the following:

- `soma_joinid`: a SOMA-defined value use for join operations.
- `dataset_id`: the dataset id as encoded in `census$get("census_info")$get("datasets")`.
- `tissue_general` and `tissue_general_ontology_term_id`: the high-level tissue mapping.

## Gene metadata

Similarly, we can obtain all gene metadata variables by directly querying the columns of the corresponding `SOMADataFrame`.

These are the variables you can use for querying the Census in case there are specific genes you are interested in.

    census$get("census_data")$get("homo_sapiens")$ms$get("RNA")$var$colnames()
    #> [1] "soma_joinid"    "feature_id"     "feature_name"   "feature_length" "nnz"
    #> [6] "n_measured_obs"

All of these variables are defined in the CELLxGENE dataset schema except for the following:

- `soma_joinid`: a SOMA-defined value use for join operations.
- `feature_length`: the length in base pairs of the gene.

## Census summary content tables

You can take a quick look at the high-level Census information by looking at `census$get("census_info")$get("summary")`:

    as.data.frame(census$get("census_info")$get("summary")$read()$concat())
    #>   soma_joinid                      label      value
    #> 1           0      census_schema_version      2.0.1
    #> 2           1          census_build_date 2024-05-20
    #> 3           2     dataset_schema_version      5.0.0
    #> 4           3           total_cell_count  115556140
    #> 5           4          unique_cell_count   60597966
    #> 6           5 number_donors_homo_sapiens      17651
    #> 7           6 number_donors_mus_musculus       4216

Of special interest are the label-value combinations for:

- `total_cell_count` is the total number of cells in the Census.
- `unique_cell_count` is the number of unique cells, as some cells may be present twice due to meta-analysis or consortia-like data.
- `number_donors_homo_sapiens` and `number_donors_mus_musculus` are the number of individuals for human and mouse. These are not guaranteed to be unique as one individual ID may be present or identical in different datasets.

### Cell counts by cell metadata

By looking at `census$get("census_info)$get("summary_cell_counts")` you can get a general idea of cell counts stratified by some relevant cell metadata. Not all cell metadata is included in this table, you can take a look at all cell and gene metadata available in the sections below “Cell metadata” and “Gene metadata”.

The line below retrieves this table and casts it into an R data frame:

    census_counts <- as.data.frame(census$get("census_info")$get("summary_cell_counts")$read()$concat())
    head(census_counts)
    #>   soma_joinid     organism category      label ontology_term_id total_cell_count
    #> 1           0 Homo sapiens      all         na               na         74322510
    #> 2           1 Homo sapiens    assay   Drop-seq      EFO:0008722           336562
    #> 3           2 Homo sapiens    assay     inDrop      EFO:0008780            51304
    #> 4           3 Homo sapiens    assay   MARS-seq      EFO:0008796            70146
    #> 5           4 Homo sapiens    assay   Seq-Well      EFO:0008919           206754
    #> 6           5 Homo sapiens    assay Smart-seq2      EFO:0008931           190792
    #>   unique_cell_count
    #> 1          44265932
    #> 2            292631
    #> 3             25652
    #> 4             70146
    #> 5             89477
    #> 6             81294

For each combination of `organism` and values for each `category` of cell metadata you can take a look at `total_cell_count` and `unique_cell_count` for the cell counts of that combination.

The values for each `category` are specified in `ontology_term_id` and `label`, which are the value’s IDs and labels, respectively.

#### Example: cell metadata included in the summary counts table

To get all the available cell metadata in the summary counts table you can do the following. Remember this is not all the cell metadata available, as some variables were omitted in the creation of this table.

    t(table(census_counts$organism, census_counts$category))
    #>
    #>                           Homo sapiens Mus musculus
    #>   all                                1            1
    #>   assay                             24           11
    #>   cell_type                        698          364
    #>   disease                          109            7
    #>   self_reported_ethnicity           31            1
    #>   sex                                3            3
    #>   suspension_type                    1            1
    #>   tissue                           267           84
    #>   tissue_general                    55           29

#### Example: cell counts for each sequencing assay in human data

To get the cell counts for each sequencing assay type in human data, you can perform the following operations:

    human_assay_counts <- census_counts[census_counts$organism == "Homo sapiens" & census_counts$category == "assay", ]
    human_assay_counts <- human_assay_counts[order(human_assay_counts$total_cell_count, decreasing = TRUE), ]

#### Example: number of microglial cells in the Census

If you have a specific term from any of the categories shown above you can directly find out the number of cells for that term.

    census_counts[census_counts$label == "microglial cell", ]
    #>      soma_joinid     organism  category           label ontology_term_id
    #> 78            77 Homo sapiens cell_type microglial cell       CL:0000129
    #> 1237        1236 Mus musculus cell_type microglial cell       CL:0000129
    #>      total_cell_count unique_cell_count
    #> 78             587981            406117
    #> 1237           119764             76113

## Understanding Census contents beyond the summary tables

While using the pre-computed tables in `census$get("census_info")` is an easy and quick way to understand the contents of the Census, it falls short if you want to learn more about certain slices of the Census.

For example, you may want to learn more about:

- What are the cell types available for human liver?
- What are the total number of cells in all lung datasets stratified by sequencing technology?
- What is the sex distribution of all cells from brain in mouse?
- What are the diseases available for T cells?

All of these questions can be answered by directly querying the cell metadata as shown in the examples below.

### Example: all cell types available in human

To exemplify the process of accessing and slicing cell metadata for summary stats, let’s start with a trivial example and take a look at all human cell types available in the Census:

    obs_df <- census$get("census_data")$get("homo_sapiens")$obs$read(column_names = c("cell_type", "is_primary_data"))
    as.data.frame(obs_df$concat())
    #>         cell_type is_primary_data
    #> 1     plasma cell           FALSE
    #> 2   mature B cell           FALSE
    #> 3     plasma cell           FALSE
    #> 4   mature B cell           FALSE
    #> 5   mature B cell           FALSE
    #> 6   mature B cell           FALSE
    #> 7   mature B cell           FALSE
    #> 8     plasma cell           FALSE
    #> 9   mature B cell           FALSE
    #> 10    plasma cell           FALSE
    #> 11  mature B cell           FALSE
    #> 12  mature B cell           FALSE
    #> 13    plasma cell           FALSE
    #> 14  mature B cell           FALSE
    #> 15    plasma cell           FALSE
    #> 16  mature B cell           FALSE
    #> 17    plasma cell           FALSE
    #> 18    plasma cell           FALSE
    #> 19  mature B cell           FALSE
    #> 20  mature B cell           FALSE
    #> 21    plasma cell           FALSE
    #> 22    plasma cell           FALSE
    #> 23    plasma cell           FALSE
    #> 24    plasma cell           FALSE
    #> 25  mature B cell           FALSE
    #> 26    plasma cell           FALSE
    #> 27  mature B cell           FALSE
    #> 28    plasma cell           FALSE
    #> 29    plasma cell           FALSE
    #> 30    plasma cell           FALSE
    #> 31    plasma cell           FALSE
    #> 32  mature B cell           FALSE
    #> 33  mature B cell           FALSE
    #> 34  mature B cell           FALSE
    #> 35  mature B cell           FALSE
    #> 36  mature B cell           FALSE
    #> 37  mature B cell           FALSE
    #> 38    plasma cell           FALSE
    #> 39  mature B cell           FALSE
    #> 40  mature B cell           FALSE
    #> 41  mature B cell           FALSE
    #> 42    plasma cell           FALSE
    #> 43    plasma cell           FALSE
    #> 44  mature B cell           FALSE
    #> 45    plasma cell           FALSE
    #> 46    plasma cell           FALSE
    #> 47  mature B cell           FALSE
    #> 48  mature B cell           FALSE
    #> 49    plasma cell           FALSE
    #> 50  mature B cell           FALSE
    #> 51  mature B cell           FALSE
    #> 52    plasma cell           FALSE
    #> 53  mature B cell           FALSE
    #> 54  mature B cell           FALSE
    #> 55    plasma cell           FALSE
    #> 56    plasma cell           FALSE
    #> 57  mature B cell           FALSE
    #> 58    plasma cell           FALSE
    #> 59  mature B cell           FALSE
    #> 60    plasma cell           FALSE
    #> 61    plasma cell           FALSE
    #> 62  mature B cell           FALSE
    #> 63  mature B cell           FALSE
    #> 64  mature B cell           FALSE
    #> 65    plasma cell           FALSE
    #> 66  mature B cell           FALSE
    #> 67    plasma cell           FALSE
    #> 68    plasma cell           FALSE
    #> 69  mature B cell           FALSE
    #> 70    plasma cell           FALSE
    #> 71  mature B cell           FALSE
    #> 72    plasma cell           FALSE
    #> 73    plasma cell           FALSE
    #> 74  mature B cell           FALSE
    #> 75    plasma cell           FALSE
    #> 76    plasma cell           FALSE
    #> 77    plasma cell           FALSE
    #> 78  mature B cell           FALSE
    #> 79    plasma cell           FALSE
    #> 80    plasma cell           FALSE
    #> 81    plasma cell           FALSE
    #> 82  mature B cell           FALSE
    #> 83    plasma cell           FALSE
    #> 84  mature B cell           FALSE
    #> 85  mature B cell           FALSE
    #> 86    plasma cell           FALSE
    #> 87  mature B cell           FALSE
    #> 88  mature B cell           FALSE
    #> 89  mature B cell           FALSE
    #> 90  mature B cell           FALSE
    #> 91    plasma cell           FALSE
    #> 92  mature B cell           FALSE
    #> 93    plasma cell           FALSE
    #> 94  mature B cell           FALSE
    #> 95  mature B cell           FALSE
    #> 96  mature B cell           FALSE
    #> 97  mature B cell           FALSE
    #> 98  mature B cell           FALSE
    #> 99  mature B cell           FALSE
    #> 100 mature B cell           FALSE
    #> 101   plasma cell           FALSE
    #> 102   plasma cell           FALSE
    #> 103   plasma cell           FALSE
    #> 104 mature B cell           FALSE
    #> 105   plasma cell           FALSE
    #> 106 mature B cell           FALSE
    #> 107 mature B cell           FALSE
    #> 108 mature B cell           FALSE
    #> 109   plasma cell           FALSE
    #> 110   plasma cell           FALSE
    #> 111   plasma cell           FALSE
    #> 112 mature B cell           FALSE
    #> 113 mature B cell           FALSE
    #> 114 mature B cell           FALSE
    #> 115 mature B cell           FALSE
    #> 116 mature B cell           FALSE
    #> 117 mature B cell           FALSE
    #> 118 mature B cell           FALSE
    #> 119   plasma cell           FALSE
    #> 120 mature B cell           FALSE
    #> 121 mature B cell           FALSE
    #> 122   plasma cell           FALSE
    #> 123   plasma cell           FALSE
    #> 124 mature B cell           FALSE
    #> 125 mature B cell           FALSE
    #> 126   plasma cell           FALSE
    #> 127   plasma cell           FALSE
    #> 128   plasma cell           FALSE
    #>  [ reached 'max' / getOption("max.print") -- omitted 74322382 rows ]

The number of rows is the total number of cells for humans. Now, if you wish to get the cell counts per cell type we can work with this data frame.

In addition, we will only focus on cells that are marked with `is_primary_data=TRUE` as this ensures we de-duplicate cells that appear more than once in CELLxGENE Discover.

    obs_df <- census$get("census_data")$get("homo_sapiens")$obs$read(
      column_names = "cell_type",
      value_filter = "is_primary_data == TRUE"
    )

    obs_df <- as.data.frame(obs_df$concat())
    nrow(obs_df)
    #> [1] 44265932

This is the number of unique cells. Now let’s look at the counts per cell type:

    human_cell_type_counts <- table(obs_df$cell_type)
    sort(human_cell_type_counts, decreasing = TRUE)[1:10]
    #>
    #>                                                    neuron
    #>                                                   2987968
    #>                                      glutamatergic neuron
    #>                                                   1604668
    #> L2/3-6 intratelencephalic projecting glutamatergic neuron
    #>                                                   1570484
    #>                                           oligodendrocyte
    #>                                                   1373223
    #>                           CD4-positive, alpha-beta T cell
    #>                                                   1368136
    #>                                                   unknown
    #>                                                   1322115
    #>                           CD8-positive, alpha-beta T cell
    #>                                                   1284243
    #>                                        classical monocyte
    #>                                                   1059249
    #>                                                    B cell
    #>                                                   1010055
    #>                                       natural killer cell
    #>                                                    931240

This shows you that the most abundant cell types are “glutamatergic neuron”, “CD8-positive, alpha-beta T cell”, and “CD4-positive, alpha-beta T cell”.

Now let’s take a look at the number of unique cell types:

    length(human_cell_type_counts)
    #> [1] 698

That is the total number of different cell types for human.

All the information in this example can be quickly obtained from the summary table at `census$get("census-info")$get("summary_cell_counts")`.

The examples below are more complex and can only be achieved by accessing the cell metadata.

### Example: cell types available in human liver

Similar to the example above, we can learn what cell types are available for a specific tissue, e.g. liver.

To achieve this goal we just need to limit our cell metadata to that tissue. We will use the information in the cell metadata variable `tissue_general`. This variable contains the high-level tissue label for all cells in the Census:

    obs_liver_df <- census$get("census_data")$get("homo_sapiens")$obs$read(
      column_names = "cell_type",
      value_filter = "is_primary_data == TRUE & tissue_general == 'liver'"
    )

    obs_liver_df <- as.data.frame(obs_liver_df$concat())

    sort(table(obs_liver_df$cell_type), decreasing = TRUE)[1:10]
    #>
    #>    periportal region hepatocyte                          T cell
    #>                           89999                           88351
    #>                      macrophage                     hepatoblast
    #>                           72769                           58447
    #>                     erythrocyte                 neoplastic cell
    #>                           57232                           52431
    #>             natural killer cell                        monocyte
    #>                           51789                           47013
    #>                    erythroblast centrilobular region hepatocyte
    #>                           46008                           45920

These are the cell types and their cell counts in the human liver.

### Example: diseased T cells in human tissues

In this example we are going to get the counts for all diseased cells annotated as T cells. For the sake of the example we will focus on “CD8-positive, alpha-beta T cell” and “CD4-positive, alpha-beta T cell”:

    obs_t_cells_df <- census$get("census_data")$get("homo_sapiens")$obs$read(
      column_names = c("disease", "tissue_general"),
      value_filter = "is_primary_data == TRUE & disease != 'normal' & cell_type %in% c('CD8-positive, alpha-beta T cell', 'CD4-positive, alpha-beta T cell')"
    )

    obs_t_cells_df <- as.data.frame(obs_t_cells_df$concat())

    print(table(obs_t_cells_df))
    #>                                                                           tissue_general
    #> disease                                                                    adipose tissue
    #>   Alzheimer disease                                                                     0
    #>   B-cell acute lymphoblastic leukemia                                                   0
    #>   B-cell non-Hodgkin lymphoma                                                           0
    #>   Barrett esophagus                                                                     0
    #>                                                                           tissue_general
    #> disease                                                                    adrenal gland
    #>   Alzheimer disease                                                                    0
    #>   B-cell acute lymphoblastic leukemia                                                  0
    #>   B-cell non-Hodgkin lymphoma                                                          0
    #>   Barrett esophagus                                                                    0
    #>                                                                           tissue_general
    #> disease                                                                    axilla
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    bladder organ
    #>   Alzheimer disease                                                                    0
    #>   B-cell acute lymphoblastic leukemia                                                  0
    #>   B-cell non-Hodgkin lymphoma                                                          0
    #>   Barrett esophagus                                                                    0
    #>                                                                           tissue_general
    #> disease                                                                     blood
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    bone marrow
    #>   Alzheimer disease                                                                  0
    #>   B-cell acute lymphoblastic leukemia                                                0
    #>   B-cell non-Hodgkin lymphoma                                                        0
    #>   Barrett esophagus                                                                  0
    #>                                                                           tissue_general
    #> disease                                                                     brain
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    breast
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    central nervous system
    #>   Alzheimer disease                                                                             0
    #>   B-cell acute lymphoblastic leukemia                                                           0
    #>   B-cell non-Hodgkin lymphoma                                                                   0
    #>   Barrett esophagus                                                                             0
    #>                                                                           tissue_general
    #> disease                                                                     colon
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    digestive system
    #>   Alzheimer disease                                                                       0
    #>   B-cell acute lymphoblastic leukemia                                                     0
    #>   B-cell non-Hodgkin lymphoma                                                             0
    #>   Barrett esophagus                                                                       0
    #>                                                                           tissue_general
    #> disease                                                                    embryo
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    endocrine gland
    #>   Alzheimer disease                                                                      0
    #>   B-cell acute lymphoblastic leukemia                                                    0
    #>   B-cell non-Hodgkin lymphoma                                                            0
    #>   Barrett esophagus                                                                      0
    #>                                                                           tissue_general
    #> disease                                                                    esophagogastric junction
    #>   Alzheimer disease                                                                               0
    #>   B-cell acute lymphoblastic leukemia                                                             0
    #>   B-cell non-Hodgkin lymphoma                                                                     0
    #>   Barrett esophagus                                                                               0
    #>                                                                           tissue_general
    #> disease                                                                    esophagus
    #>   Alzheimer disease                                                                0
    #>   B-cell acute lymphoblastic leukemia                                              0
    #>   B-cell non-Hodgkin lymphoma                                                      0
    #>   Barrett esophagus                                                                0
    #>                                                                           tissue_general
    #> disease                                                                    exocrine gland
    #>   Alzheimer disease                                                                     0
    #>   B-cell acute lymphoblastic leukemia                                                   0
    #>   B-cell non-Hodgkin lymphoma                                                           0
    #>   Barrett esophagus                                                                     0
    #>                                                                           tissue_general
    #> disease                                                                       eye
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    fallopian tube
    #>   Alzheimer disease                                                                     0
    #>   B-cell acute lymphoblastic leukemia                                                   0
    #>   B-cell non-Hodgkin lymphoma                                                           0
    #>   Barrett esophagus                                                                     0
    #>                                                                           tissue_general
    #> disease                                                                    gallbladder
    #>   Alzheimer disease                                                                  0
    #>   B-cell acute lymphoblastic leukemia                                                0
    #>   B-cell non-Hodgkin lymphoma                                                        0
    #>   Barrett esophagus                                                                  0
    #>                                                                           tissue_general
    #> disease                                                                     heart
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    immune system
    #>   Alzheimer disease                                                                    0
    #>   B-cell acute lymphoblastic leukemia                                                  0
    #>   B-cell non-Hodgkin lymphoma                                                          0
    #>   Barrett esophagus                                                                    0
    #>                                                                           tissue_general
    #> disease                                                                    intestine
    #>   Alzheimer disease                                                                0
    #>   B-cell acute lymphoblastic leukemia                                              0
    #>   B-cell non-Hodgkin lymphoma                                                      0
    #>   Barrett esophagus                                                                0
    #>                                                                           tissue_general
    #> disease                                                                    kidney
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    lamina propria
    #>   Alzheimer disease                                                                     0
    #>   B-cell acute lymphoblastic leukemia                                                   0
    #>   B-cell non-Hodgkin lymphoma                                                           0
    #>   Barrett esophagus                                                                     0
    #>                                                                           tissue_general
    #> disease                                                                    large intestine
    #>   Alzheimer disease                                                                      0
    #>   B-cell acute lymphoblastic leukemia                                                    0
    #>   B-cell non-Hodgkin lymphoma                                                            0
    #>   Barrett esophagus                                                                      0
    #>                                                                           tissue_general
    #> disease                                                                     liver
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                      lung
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    lymph node
    #>   Alzheimer disease                                                                 0
    #>   B-cell acute lymphoblastic leukemia                                               0
    #>   B-cell non-Hodgkin lymphoma                                                       0
    #>   Barrett esophagus                                                                 0
    #>                                                                           tissue_general
    #> disease                                                                    mucosa
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    musculature
    #>   Alzheimer disease                                                                  0
    #>   B-cell acute lymphoblastic leukemia                                                0
    #>   B-cell non-Hodgkin lymphoma                                                        0
    #>   Barrett esophagus                                                                  0
    #>                                                                           tissue_general
    #> disease                                                                      nose
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    omentum
    #>   Alzheimer disease                                                              0
    #>   B-cell acute lymphoblastic leukemia                                            0
    #>   B-cell non-Hodgkin lymphoma                                                    0
    #>   Barrett esophagus                                                              0
    #>                                                                           tissue_general
    #> disease                                                                     ovary
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    pancreas
    #>   Alzheimer disease                                                               0
    #>   B-cell acute lymphoblastic leukemia                                             0
    #>   B-cell non-Hodgkin lymphoma                                                     0
    #>   Barrett esophagus                                                               0
    #>                                                                           tissue_general
    #> disease                                                                    placenta
    #>   Alzheimer disease                                                               0
    #>   B-cell acute lymphoblastic leukemia                                             0
    #>   B-cell non-Hodgkin lymphoma                                                     0
    #>   Barrett esophagus                                                               0
    #>                                                                           tissue_general
    #> disease                                                                    pleura
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    pleural fluid
    #>   Alzheimer disease                                                                    0
    #>   B-cell acute lymphoblastic leukemia                                                  0
    #>   B-cell non-Hodgkin lymphoma                                                          0
    #>   Barrett esophagus                                                                    0
    #>                                                                           tissue_general
    #> disease                                                                    prostate gland
    #>   Alzheimer disease                                                                     0
    #>   B-cell acute lymphoblastic leukemia                                                   0
    #>   B-cell non-Hodgkin lymphoma                                                           0
    #>   Barrett esophagus                                                                     0
    #>                                                                           tissue_general
    #> disease                                                                    reproductive system
    #>   Alzheimer disease                                                                          0
    #>   B-cell acute lymphoblastic leukemia                                                        0
    #>   B-cell non-Hodgkin lymphoma                                                                0
    #>   Barrett esophagus                                                                          0
    #>                                                                           tissue_general
    #> disease                                                                    respiratory system
    #>   Alzheimer disease                                                                         0
    #>   B-cell acute lymphoblastic leukemia                                                       0
    #>   B-cell non-Hodgkin lymphoma                                                               0
    #>   Barrett esophagus                                                                         0
    #>                                                                           tissue_general
    #> disease                                                                    saliva
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                     scalp
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    skeletal system
    #>   Alzheimer disease                                                                      0
    #>   B-cell acute lymphoblastic leukemia                                                    0
    #>   B-cell non-Hodgkin lymphoma                                                            0
    #>   Barrett esophagus                                                                      0
    #>                                                                           tissue_general
    #> disease                                                                    skin of body
    #>   Alzheimer disease                                                                   0
    #>   B-cell acute lymphoblastic leukemia                                                 0
    #>   B-cell non-Hodgkin lymphoma                                                         0
    #>   Barrett esophagus                                                                   0
    #>                                                                           tissue_general
    #> disease                                                                    small intestine
    #>   Alzheimer disease                                                                      0
    #>   B-cell acute lymphoblastic leukemia                                                    0
    #>   B-cell non-Hodgkin lymphoma                                                            0
    #>   Barrett esophagus                                                                      0
    #>                                                                           tissue_general
    #> disease                                                                    spinal cord
    #>   Alzheimer disease                                                                  0
    #>   B-cell acute lymphoblastic leukemia                                                0
    #>   B-cell non-Hodgkin lymphoma                                                        0
    #>   Barrett esophagus                                                                  0
    #>                                                                           tissue_general
    #> disease                                                                    spleen
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    stomach
    #>   Alzheimer disease                                                              0
    #>   B-cell acute lymphoblastic leukemia                                            0
    #>   B-cell non-Hodgkin lymphoma                                                    0
    #>   Barrett esophagus                                                              0
    #>                                                                           tissue_general
    #> disease                                                                    tendon of semitendinosus
    #>   Alzheimer disease                                                                               0
    #>   B-cell acute lymphoblastic leukemia                                                             0
    #>   B-cell non-Hodgkin lymphoma                                                                     0
    #>   Barrett esophagus                                                                               0
    #>                                                                           tissue_general
    #> disease                                                                    testis
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    tongue
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    ureter
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    uterus
    #>   Alzheimer disease                                                             0
    #>   B-cell acute lymphoblastic leukemia                                           0
    #>   B-cell non-Hodgkin lymphoma                                                   0
    #>   Barrett esophagus                                                             0
    #>                                                                           tissue_general
    #> disease                                                                    vasculature
    #>   Alzheimer disease                                                                  0
    #>   B-cell acute lymphoblastic leukemia                                                0
    #>   B-cell non-Hodgkin lymphoma                                                        0
    #>   Barrett esophagus                                                                  0
    #>                                                                           tissue_general
    #> disease                                                                    yolk sac
    #>   Alzheimer disease                                                               0
    #>   B-cell acute lymphoblastic leukemia                                             0
    #>   B-cell non-Hodgkin lymphoma                                                     0
    #>   Barrett esophagus                                                               0
    #>  [ reached getOption("max.print") -- omitted 105 rows ]

These are the cell counts annotated with the indicated disease across human tissues for “CD8-positive, alpha-beta T cell” or “CD4-positive, alpha-beta T cell”.