Interacting with domino Objects

Source: vignettes/domino_object_vignette.Rmd

In this tutorial, we will go into more detail on the structure of a domino object and the ways in which to access the data stored within. We will be using the domino object we built on the Getting Started page. If you have not yet built a domino object, you can do so by following the instructions on the Getting Started page.

Instructions to load data 
set.seed(42)
library(dominoSignal)

# BiocFileCache helps with file management across sessions
bfc <- BiocFileCache::BiocFileCache(ask = FALSE)
data_url <- "https://zenodo.org/records/10951634/files/pbmc_domino_built.rds"
tmp_path <- BiocFileCache::bfcrpath(bfc, data_url)
dom <- readRDS(tmp_path)

Object contents

There is a great deal of information stored with the domino object class. The domino object is an S4 class object that contains a variety of information about the data set used to build the object, the calculated values, and the linkages between receptors, ligands, and transcription factors. The object is structured as follows (with some examples of the information stored within each slot:

  • Input Data

    • Information about the database used to construct the rl_map

    • Inputted counts matrix

    • Inputted z-scored counts matrix

    • Inputted cluster labels

    • Inputted transcription factor activation scores

  • Calculated values

    • Differential expression p-values of transcription factors in each cluster

    • Correlation values between ligands and receptors

    • Median correlation between components of receptor complexes

  • Linkages

    • Complexes show the component genes of any complexes in the rl map

    • Receptor - ligand linkages as determined from the rl map

    • Transcription factor - target linkages as determined from the SCENIC analysis (or other regulon inference method)

    • Transcription factors that are differentially expressed in each cluster

    • Transcription factors that are correlated with receptors

    • Transcription factors that are correlated with receptors in each cluster

    • Receptors which are active in each cluster

    • Ligands that may activate a receptor in a given cluster (so-called incoming ligands; these may include ligands from outside the data set)

  • Signaling matrices

    • For each cluster, incoming ligands and the clusters within the data set that they are coming from

    • A summary of signaling between all clusters

  • Miscellaneous Information

    • Build information, which includes the parameters used to build the object in the build_domino() functions

    • The pared down receptor ligand map information used in building the object

    • The percent expression of receptors within each cluster

For commonly accessed information (the number of cells, clusters, and some build information), the show and print methods for domino objects can be used.

dom
#> A domino object of 2607 cells
#> Built with signaling between 9 clusters
print(dom)

Access functions

To facilitate access to the information stored in the domino object, we have provided a collection of functions to retrieve specific items. These functions begin with “dom_” and can be listed using ls().

ls("package:dominoSignal", pattern = "^dom_")
#>  [1] "dom_clusters"      "dom_correlations"  "dom_counts"       
#>  [4] "dom_database"      "dom_de"            "dom_info"         
#>  [7] "dom_linkages"      "dom_network_items" "dom_signaling"    
#> [10] "dom_tf_activation" "dom_zscores"

Input data

When creating a domino object with the create_domino() function, several inputs are required which are then stored in the domino object itself. These include cluster labels, the counts matrix, z-scored counts matrix, transcription factor activation scores, and the R-L database used in create_rl_map_cellphonedb().

For example, to access the cluster names in the domino object:

dom_clusters(dom)
#> [1] "B_cell"            "CD14_monocyte"     "CD16_monocyte"    
#> [4] "CD8_T_cell"        "dendritic_cell"    "memory_CD4_T_cell"
#> [7] "naive_CD4_T_cell"  "NK_cell"           "Platelet"

Setting an argument labels = TRUE will return the vector of cluster labels for each cell rather than the unique cluster names.

To access the counts:

count_matrix <- dom_counts(dom)
knitr::kable(count_matrix[1:5, 1:5])
AAACATACAACCAC-1 AAACATTGAGCTAC-1 AAACATTGATCAGC-1 AAACCGTGCTTCCG-1 AAACCGTGTATGCG-1
AL627309.1 0 0 0 0 0
AP006222.2 0 0 0 0 0
RP11-206L10.2 0 0 0 0 0
RP11-206L10.9 0 0 0 0 0
FAM87B 0 0 0 0 0

Or z-scored counts:

z_matrix <- dom_zscores(dom)
knitr::kable(z_matrix[1:5, 1:5])
AAACATACAACCAC-1 AAACATTGAGCTAC-1 AAACATTGATCAGC-1 AAACCGTGCTTCCG-1 AAACCGTGTATGCG-1
AL627309.1 -0.0581122 -0.0581122 -0.0581122 -0.0581122 -0.0581122
AP006222.2 -0.0335151 -0.0335151 -0.0335151 -0.0335151 -0.0335151
RP11-206L10.2 -0.0399375 -0.0399375 -0.0399375 -0.0399375 -0.0399375
RP11-206L10.9 -0.0337574 -0.0337574 -0.0337574 -0.0337574 -0.0337574
FAM87B -0.0274227 -0.0274227 -0.0274227 -0.0274227 -0.0274227

The transcription factor activation scores can be similarly accessed:

activation_matrix <- dom_tf_activation(dom)
knitr::kable(activation_matrix[1:5, 1:5])
AAACATACAACCAC-1 AAACATTGAGCTAC-1 AAACATTGATCAGC-1 AAACCGTGCTTCCG-1 AAACCGTGTATGCG-1
ARNTL 0.0446386 0.0413253 0.0441566 0.0437952 0.1087952
ATF3 0.0582029 0.0870623 0.0509289 0.1172953 0.0638104
ATF4 0.0295733 0.0437047 0.0542889 0.0427879 0.0436855
ATF6 0.0000000 0.0211198 0.1151665 0.0850461 0.0460666
BCL3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

Information about the database referenced for ligand - receptor pairs and composition of protein complexes can be extracted from the dom_database() function. By default, the function returns the name(s) of the database(s) used:

dom_database(dom)
#> [1] "CellPhoneDB_v4.0"

If you would like to view the entire ligand - receptor map, set name_only = FALSE:

db_matrix <- dom_database(dom, name_only = FALSE)
knitr::kable(db_matrix[1:5, 1:5])
int_pair name_A uniprot_A gene_A type_A
4 RAreceptor_RXRG & atRetinoicAcid_byALDH1A3 RAreceptor_RXRG P48443,P29373 RXRG,CRABP2 R
5 RAreceptor_RXRG & atRetinoicAcid_byALDH1A2 RAreceptor_RXRG P48443,P29373 RXRG,CRABP2 R
6 RAreceptor_RXRG & atRetinoicAcid_byALDH1A1 RAreceptor_RXRG P48443,P29373 RXRG,CRABP2 R
7 RAreceptor_RXRB & atRetinoicAcid_byALDH1A3 RAreceptor_RXRB P28702,P29373 RXRB,CRABP2 R
8 RAreceptor_RXRB & atRetinoicAcid_byALDH1A2 RAreceptor_RXRB P28702,P29373 RXRB,CRABP2 R

Calculations

Active transcription factors in each cluster are determined by conducting Wilcoxon rank sum tests for each transcription factor where the transcription factor activity scores amongst all cells in a cluster are tested against the activity scores of all cells outside of the cluster. The p-values for the one-sided test for greater activity within the cluster compared to other cells can be accessed with the dom_de() function.

de_matrix <- dom_de(dom)
knitr::kable(de_matrix[1:5, 1:5])
B_cell CD14_monocyte CD16_monocyte CD8_T_cell dendritic_cell
ARNTL 0.0000019 1 0.9947780 0.9865518 0.8359381
ATF3 0.0006972 0 0.0000000 1.0000000 0.0000000
ATF4 0.8399818 1 1.0000000 0.9631934 0.1748338
ATF6 0.5988625 1 0.9893142 0.0365779 0.9549489
BCL3 0.9299696 0 0.6007326 0.1482247 0.0757460

Linkage between receptors and transcription factors is assessed by Spearman correlation between transcription factor activity scores and scaled expression of receptor-encoding genes across all cells in the data set. Spearman coefficients can be accessed with the dom_correlations() function. Setting type to “complex” will return the median correlation between components of receptor complexes; the default (“rl”) will return receptor - ligand correlations.

cor_matrix <- dom_correlations(dom)
knitr::kable(cor_matrix[1:5, 1:5])
ARNTL ATF3 ATF4 ATF6 BCL3
TNFRSF18 0.0057014 -0.0297120 0.0043825 0.0063055 -0.0029035
TNFRSF4 0.0373481 -0.1012705 0.0344042 0.0508720 0.0282500
TNFRSF14 -0.0356892 0.0541435 0.0015811 0.0093978 0.0206700
TNFRSF25 0.0310362 -0.1171502 0.0701541 0.0458227 0.0047186
TNFRSF1B -0.0933019 0.2690328 -0.0625319 -0.0457366 0.0239629

Linkages

Linkages between ligands, receptors, and transcription factors can be accessed in several different ways, depending on the specific link and the scope desired. The dom_linkages() function has three arguments - the first, like all of our access functions, is for the domino object. The second, link_type, is used to specify which linkages are desired (options are complexes, receptor - ligand, tf - target, or tf - receptor). The third argument, by_cluster, determines whether the linkages returned are arranged by cluster (though this does change the available linkage types to tf - receptor, receptor, or incoming-ligand). For example, to access the complexes used across the dataset:

complex_links <- dom_linkages(dom, link_type = "complexes")
# Look for components of NODAL receptor complex
complex_links$NODAL_receptor
#> NULL

To view incoming ligands to each cluster:

incoming_links <- dom_linkages(dom, link_type = "incoming-ligand", by_cluster = TRUE)
# Check incoming signals to dendritic cells
incoming_links$dendritic_cell
#>  [1] "COPA"                  "MIF"                   "APP"                  
#>  [4] "FAM19A4"               "TAFA4"                 "ANXA1"                
#>  [7] "CD99"                  "integrin_aVb3_complex" "integrin_a4b1_complex"
#> [10] "BMP8B"                 "PLAU"                  "CSF3"                 
#> [13] "CXCL9"                 "HLA-F"                 "CD1D"                 
#> [16] "INS"                   "IL34"                  "CSF1"                 
#> [19] "CSF2"                  "CTLA4"                 "CD28"                 
#> [22] "GRN"                   "TNF"                   "LTA"                  
#> [25] "CXCL12"                "CXCL14"                "CD58"

If, for some reason, you find yourself in need of the entire linkage structure (not recommended), it can be accessed through its slot name; domino objects are S4 objects.

all_linkages <- slot(dom, "linkages")
# Names of all sub-structures:
names(all_linkages)
#> [1] "complexes"          "rec_lig"            "tf_targets"        
#> [4] "clust_tf"           "tf_rec"             "clust_tf_rec"      
#> [7] "clust_rec"          "clust_incoming_lig"

Alternately, to obtain a simplified list of receptors, ligands, and/or features in the domino object, use the dom_network_items() function. To pull all transcription factors associated with the dendritic cell cluster:

dc_tfs <- dom_network_items(dom, "dendritic_cell", return = "features")
head(dc_tfs)
#> [1] "ATF3"  "CEBPD" "FOSB"  "STAT6" "KLF4"  "CEBPA"

Signaling Matrices

The averaged z-scored expression of ligands and receptors between different clusters can be accessed in matrix form.

signal_matrix <- dom_signaling(dom)
knitr::kable(signal_matrix)
L_B_cell L_CD14_monocyte L_CD16_monocyte L_CD8_T_cell L_dendritic_cell L_memory_CD4_T_cell L_naive_CD4_T_cell L_NK_cell L_Platelet
R_B_cell 0.0494729 0.1976263 0.1686996 0.0000000 0.3040989 0.2459618 0.1367747 0.0000000 4.013299
R_CD14_monocyte 0.8060665 2.5378490 1.4429140 1.1787148 3.4961650 2.2611486 1.2608492 1.4485708 10.559449
R_CD16_monocyte 0.8060665 2.5378490 1.1473216 1.1787148 3.4961650 2.2611486 0.8757246 1.4055805 7.258572
R_CD8_T_cell 0.3759111 0.0000000 0.1263349 0.2120444 0.0000000 0.2772703 0.0000000 0.1604005 0.000000
R_dendritic_cell 0.3176857 2.5041485 0.7368126 1.3152485 3.4961650 2.3809976 0.3061580 1.5659811 7.258572
R_memory_CD4_T_cell 0.3759111 0.0000000 0.1263349 0.2120444 0.0000000 0.3801282 0.0000000 0.1604005 0.000000
R_naive_CD4_T_cell 0.3759111 0.0000000 0.1263349 0.2120444 0.0000000 0.3801282 0.0000000 0.1604005 0.000000
R_NK_cell 0.2930600 1.5760509 0.6086536 0.2556741 1.5025648 0.7620921 0.1772729 0.1604005 4.013299
R_Platelet 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.000000

To view signaling to a specific cluster from the other clusters, set the cluster argument to the cluster name.

dc_matrix <- dom_signaling(dom, "dendritic_cell")
knitr::kable(dc_matrix)
dendritic_cell.L_B_cell dendritic_cell.L_CD14_monocyte dendritic_cell.L_CD16_monocyte dendritic_cell.L_CD8_T_cell dendritic_cell.L_dendritic_cell dendritic_cell.L_memory_CD4_T_cell dendritic_cell.L_naive_CD4_T_cell dendritic_cell.L_NK_cell dendritic_cell.L_Platelet
COPA 0.0000000 0.1352458 0.1686996 0.0000000 0.1706852 0.0243003 0.0000000 0.0000000 0.1634935
MIF 0.0000000 0.0000000 0.0000000 0.0000000 0.0810828 0.1637432 0.1367747 0.0000000 0.0000000
APP 0.0494729 0.0623805 0.0000000 0.0000000 0.0523309 0.0579182 0.0000000 0.0000000 3.8498060
ANXA1 0.0000000 0.1864958 0.0000000 0.1682595 0.6876552 0.5065038 0.0000000 0.3542401 0.0000000
CD99 0.0000000 0.0626658 0.0000000 0.4718174 0.0000000 0.1952307 0.0000000 0.7924524 1.9983051
integrin_a4b1_complex 0.0775377 0.0000000 0.0274081 0.0128595 0.0933263 0.1408531 0.0000000 0.0000000 1.2469674
BMP8B 0.1291568 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
PLAU 0.0000000 0.0455798 0.0000000 0.0711901 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
CXCL9 0.0000000 0.0663249 0.0000000 0.0000000 0.0000000 0.0582573 0.0000000 0.0000000 0.0000000
HLA-F 0.0000000 0.0000000 0.0000000 0.2918047 0.0000000 0.0000000 0.0000000 0.2588880 0.0000000
CD1D 0.0615183 0.5670314 0.1007509 0.0000000 1.2126187 0.0000000 0.0000000 0.0000000 0.0000000
CSF1 0.0000000 0.0000000 0.0000000 0.0067252 0.0000000 0.1724684 0.0000000 0.0000000 0.0000000
CTLA4 0.0000000 0.0000000 0.0000000 0.0369179 0.0000000 0.2085753 0.0000000 0.0000000 0.0000000
CD28 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.2771802 0.1288850 0.0000000 0.0000000
GRN 0.0000000 1.3784246 0.2818176 0.0000000 1.1878101 0.0000000 0.0000000 0.0000000 0.0000000
TNF 0.0000000 0.0000000 0.0318015 0.1191403 0.0106558 0.1381279 0.0000000 0.0000000 0.0000000
LTA 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.1828448 0.0404983 0.0000000 0.0000000
CXCL12 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.1028579 0.0000000 0.0000000 0.0000000
CD58 0.0000000 0.0000000 0.1263349 0.1365337 0.0000000 0.1521363 0.0000000 0.1604005 0.0000000

Build information

To keep track of the options set when running build_domino(), they are stored within the domino object itself. To view these options, use the dom_info() function.

dom_info(dom)
#> $create
#> [1] TRUE
#> 
#> $build
#> [1] TRUE
#> 
#> $build_variables
#>     max_tf_per_clust          min_tf_pval       max_rec_per_tf 
#>               25.000                0.001               25.000 
#> rec_tf_cor_threshold   min_rec_percentage 
#>                0.250                0.100

Continued Development

Since dominoSignal is a package still being developed, there are new functions and features that will be implemented in future versions. In the meantime, we have put together further information on plotting and an example analysis can be viewed on our Getting Started page. Additionally, if you find any bugs, have further questions, or want to share an idea, please let us know here.

Vignette Build Information

Date last built and session information:

Sys.Date()
#> [1] "2024-11-20"
sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] dominoSignal_1.0.1
#> 
#> loaded via a namespace (and not attached):
#>   [1] DBI_1.2.3               httr2_1.0.6             formatR_1.14           
#>   [4] biomaRt_2.62.0          rlang_1.1.4             magrittr_2.0.3         
#>   [7] clue_0.3-66             GetoptLong_1.0.5        matrixStats_1.4.1      
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#>  [31] cachem_1.1.0            GenomeInfoDb_1.42.0     jsonlite_1.8.9         
#>  [34] progress_1.2.3          blob_1.2.4              broom_1.0.7            
#>  [37] parallel_4.4.2          prettyunits_1.2.0       cluster_2.1.6          
#>  [40] R6_2.5.1                bslib_0.8.0             stringi_1.8.4          
#>  [43] RColorBrewer_1.1-3      car_3.1-3               jquerylib_0.1.4        
#>  [46] Rcpp_1.0.13-1           iterators_1.0.14        knitr_1.49             
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#>  [64] evaluate_1.0.1          desc_1.4.3              BiocFileCache_2.14.0   
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#>  [73] carData_3.0-5           foreach_1.5.2           stats4_4.4.2           
#>  [76] generics_0.1.3          S4Vectors_0.44.0        hms_1.1.3              
#>  [79] ggplot2_3.5.1           munsell_0.5.1           scales_1.3.0           
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#>  [85] fs_1.6.5                grid_4.4.2              tidyr_1.3.1            
#>  [88] AnnotationDbi_1.68.0    colorspace_2.1-1        GenomeInfoDbData_1.2.13
#>  [91] Formula_1.2-5           cli_3.6.3               rappdirs_0.3.3         
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