Creates a linkage_summary() object storing the linkages learned in different domino objects as nested lists to facilitate comparisons of networks learned by domino across subject covariates.
Arguments
- domino_results
list of domino result with one domino object per subject. Names from the list must match subject_names
- subject_meta
data frame that includes the subject features by which the objects could be grouped. The first column should must be subject names
- subject_names
vector of subject names in domino_results. If NULL, defaults to first column of subject_meta.
Value
A linkage summary class object consisting of nested lists of the active transcription factors, active receptors, and incoming ligands for each cluster across multiple domino results
Examples
example(build_domino, echo = FALSE)
#create alternative clustering by shuffling cluster assignments
clusters_tiny_alt <- setNames(
PBMC$clusters_tiny[c(121:240, 1:120, 241:360)],
names(PBMC$clusters_tiny)
)
clusters_tiny_alt <- as.factor(clusters_tiny_alt)
#build an alternative domino object
pbmc_dom_tiny_alt <- create_domino(
rl_map = rl_map_tiny,
features = SCENIC$auc_tiny,
counts = PBMC$RNA_count_tiny,
z_scores = PBMC$RNA_zscore_tiny,
clusters = clusters_tiny_alt,
tf_targets = regulon_list_tiny,
use_clusters = TRUE,
use_complexes = TRUE,
remove_rec_dropout = FALSE
)
#> Reading in and processing signaling database
#> Database provided from source: CellPhoneDB
#> Getting z_scores, clusters, and counts
#> Calculating feature enrichment by cluster
#> 1 of 3
#> 2 of 3
#> 3 of 3
#> Calculating correlations
#> 1 of 6
#> 2 of 6
#> 3 of 6
#> 4 of 6
#> 5 of 6
#> 6 of 6
pbmc_dom_built_tiny_alt <- build_domino(
dom = pbmc_dom_tiny_alt,
min_tf_pval = .05,
max_tf_per_clust = Inf,
max_rec_per_tf = Inf,
rec_tf_cor_threshold = .1,
min_rec_percentage = 0.01
)
#create a list of domino objects
dom_ls <- list(
dom1 = pbmc_dom_built_tiny,
dom2 = pbmc_dom_built_tiny_alt
)
#compare the linkages across the two domino objects
meta_df <- data.frame("ID" = c("dom1", "dom2"), "group" = c("A", "B"))
summarize_linkages(
domino_results = dom_ls, subject_meta = meta_df,
subject_names = meta_df$ID
)
#> An object of class "linkage_summary"
#> Slot "subject_names":
#> [1] dom1 dom2
#> Levels: dom1 dom2
#>
#> Slot "subject_meta":
#> ID group
#> 1 dom1 A
#> 2 dom2 B
#>
#> Slot "subject_linkages":
#> $dom1
#> $dom1$B_cell
#> $dom1$B_cell$tfs
#> character(0)
#>
#> $dom1$B_cell$rec
#> NULL
#>
#> $dom1$B_cell$incoming_lig
#> NULL
#>
#> $dom1$B_cell$tfs_rec
#> character(0)
#>
#> $dom1$B_cell$rec_lig
#> character(0)
#>
#>
#> $dom1$CD14_monocyte
#> $dom1$CD14_monocyte$tfs
#> [1] "ZNF324" "CREM" "FOSL1"
#>
#> $dom1$CD14_monocyte$rec
#> [1] "CXCR3" "IL7_receptor" "TGFBR3" "NRG1"
#>
#> $dom1$CD14_monocyte$incoming_lig
#> [1] "CCL20" "IL7" "TGFB3"
#> [4] "integrin_a6b4_complex"
#>
#> $dom1$CD14_monocyte$tfs_rec
#> [1] "ZNF324 <- CXCR3" "CREM <- IL7_receptor" "CREM <- TGFBR3"
#> [4] "FOSL1 <- NRG1"
#>
#> $dom1$CD14_monocyte$rec_lig
#> [1] "CXCR3 <- CCL20" "IL7_receptor <- IL7"
#> [3] "TGFBR3 <- TGFB3" "NRG1 <- integrin_a6b4_complex"
#>
#>
#> $dom1$CD8_T_cell
#> $dom1$CD8_T_cell$tfs
#> [1] "FLI1"
#>
#> $dom1$CD8_T_cell$rec
#> [1] "CXCR3" "IL7_receptor"
#>
#> $dom1$CD8_T_cell$incoming_lig
#> [1] "CCL20" "IL7"
#>
#> $dom1$CD8_T_cell$tfs_rec
#> [1] "FLI1 <- CXCR3" "FLI1 <- IL7_receptor"
#>
#> $dom1$CD8_T_cell$rec_lig
#> [1] "CXCR3 <- CCL20" "IL7_receptor <- IL7"
#>
#>
#>
#> $dom2
#> $dom2$B_cell
#> $dom2$B_cell$tfs
#> character(0)
#>
#> $dom2$B_cell$rec
#> NULL
#>
#> $dom2$B_cell$incoming_lig
#> NULL
#>
#> $dom2$B_cell$tfs_rec
#> character(0)
#>
#> $dom2$B_cell$rec_lig
#> character(0)
#>
#>
#> $dom2$CD14_monocyte
#> $dom2$CD14_monocyte$tfs
#> [1] "FLI1"
#>
#> $dom2$CD14_monocyte$rec
#> [1] "CXCR3" "IL7_receptor"
#>
#> $dom2$CD14_monocyte$incoming_lig
#> [1] "CCL20" "IL7"
#>
#> $dom2$CD14_monocyte$tfs_rec
#> [1] "FLI1 <- CXCR3" "FLI1 <- IL7_receptor"
#>
#> $dom2$CD14_monocyte$rec_lig
#> [1] "CXCR3 <- CCL20" "IL7_receptor <- IL7"
#>
#>
#> $dom2$CD8_T_cell
#> $dom2$CD8_T_cell$tfs
#> [1] "ZNF324" "CREM" "FOSL1"
#>
#> $dom2$CD8_T_cell$rec
#> [1] "CXCR3" "IL7_receptor" "TGFBR3" "NRG1"
#>
#> $dom2$CD8_T_cell$incoming_lig
#> [1] "CCL20" "IL7" "TGFB3"
#> [4] "integrin_a6b4_complex"
#>
#> $dom2$CD8_T_cell$tfs_rec
#> [1] "ZNF324 <- CXCR3" "CREM <- IL7_receptor" "CREM <- TGFBR3"
#> [4] "FOSL1 <- NRG1"
#>
#> $dom2$CD8_T_cell$rec_lig
#> [1] "CXCR3 <- CCL20" "IL7_receptor <- IL7"
#> [3] "TGFBR3 <- TGFB3" "NRG1 <- integrin_a6b4_complex"
#>
#>
#>
#>