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Determining Donor and Recipient Cells

2025-05-12

donor_recipient.Rmd

Creating a new variantCell project

If you haven’t already done so, you can create a new project by using the command:

#Create new variantCell object
project <- variantCell$new()

to initialize the project.

Determining Donor / Recipient Cells in Single Cell Data

If you need to identify which cells are donor or recipient, you can use the process_vireo_seurat helper function (below).

#process vireo using Seurat metadata
process_vireo_seurat = function(
  seurat_obj,
  vireo_path,
  prefix_text
)

Usage example:

sample_donor_recipient <- vCell_project$process_vireo_seurat(
    sample,
    vireo_path  = "donor_ids.tsv",
    prefix_text = "prefix_text_to_add_"
)

This will provide output similar to below, indicating the matching cells in the metadata, and the cell type distribution for the donors identified by Vireo:

Initial cell identities in Seurat object:

Sample1 1152 Seurat object cells: 1152 Total Vireo cells: 1661

First few Seurat rownames: Patient1_AAACCCAAGTCTAGAA-1 Patient1_AAACGCTGTGGACAGT-1 Patient1_AAAGGATCAGTTGTTG-1 Patient1_AAAGGATTCCTCGCAT-1 Patient1_AAAGTCCAGCACTCCG-1 Patient1_AAAGTCCGTTGCATTG-1 First few metadata rownames: Patient1_AAACCCAAGTCTAGAA-1 Patient1_AAACGCTGTGGACAGT-1 Patient1_AAAGGATCAGTTGTTG-1 Patient1_AAAGGATTCCTCGCAT-1 Patient1_AAAGGGCTCAAAGGTA-1 Patient1_AAAGTCCAGCACTCCG-1

Number of matching cells: 1152

Cell type distribution for donor1:

  Classical Monocyte        Differentiating T            Gamma Delta T        IGSF21+ Dendritic 
                  10                       34                       81                        9 
     Innate Lymphoid    Intermediate Monocyte               Macrophage                     MAIT 
                   4                        3                       29                        5 
                Mast                 Memory B Myeloid Dendritic Type 1 Myeloid Dendritic Type 2 
                  13                       46                       10                       23 
             Naive B             Naive CD4+ T             Naive CD8+ T               Neutrophil 
                   1                       31                        2                        1 
                  NK    Nonclassical Monocyte OLR1+ Classical Monocyte                   Plasma 
                  14                       23                        2                       62

Cell type distribution for donor0:

Adventitial Fibroblast       Airway Smooth Muscle Alveolar Epithelial Type 1 Alveolar Epithelial Type 2 
                     5                          1                          3                          1 
   Alveolar Fibroblast                     Artery                      Basal                  Capillary 
                    13                         10                         16                         38 
    Capillary Aerocyte                   Ciliated      Differentiating Basal                     Goblet 
                     3                          3                          1                          1 
             Lymphatic           Microvasculature                     Mucous              Myofibroblast 
                     1                         11                          1                          3 
              Pericyte                     Plasma        Proliferating Basal             Proximal Basal 
                     6                          3                          2                          3 
Vascular Smooth Muscle                       Vein 
                     3                         11

In this case, the donor cells can be identified as (likely) donor0 - with predominantly structural lung cells, while donor1, containing mostly immune cells, is the recipient. This will be used as input to the addSampleData function - to specify which donor is the recipient/donor. This process will need to be repeated for each sample to determine donor/recipient, based on cell type distributions.