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Detect Tertiary Lymphoid Structures using a KNN-density approach

detect_TLS.Rd

Identifies TLS candidates by finding regions of high local B-cell density that also contain a sufficient number of nearby T cells (B+T co-localisation). Phenotype labels "B cell" and "B cells" (and their T-cell equivalents) are both accepted.

Usage

detect_TLS(
  LSP,
  ldata,
  k = 30L,
  bcell_density_threshold = 10,
  min_B_cells = 50L,
  min_T_cells_nearby = 10L,
  max_distance_T = 50,
  expand_distance = 80
)

Arguments

LSP

Character. Sample name in ldata.

k

Integer. Number of nearest neighbours used for density estimation (default 30, calibrated for 0.325 um/px imaging).

bcell_density_threshold

Numeric. Minimum average 1/k-distance (in microns) for a B cell to be considered locally dense (default 15).

min_B_cells

Integer. Minimum B cells per candidate TLS cluster (default 50).

min_T_cells_nearby

Integer. Minimum T cells within max_distance_T microns of the candidate cluster centre (default 30).

max_distance_T

Numeric. Search radius (microns) for T-cell proximity check (default 50).

expand_distance

Integer. The extended values from the boundary of the deteced B-cells clusters that the T cells are bieng integrated (default 80).

ldata

Named list of data frames, or NULL to use the global ldata object (deprecated; pass explicitly).

Value

The similarly formatted ldata list, with the data frame for LSP augmented by three new columns:

tls_id_knn

Integer. 0 = non-TLS cell; positive integer = TLS cluster ID.

tls_center_x

Numeric. X coordinate of the TLS centre for TLS cells; NA otherwise.

tls_center_y

Numeric. Y coordinate of the TLS centre for TLS cells; NA otherwise.

Examples

data(toy_ldata)
ldata <- detect_TLS("ToySample", k = 30, ldata = toy_ldata)
#> Detected TLS: 2
table(ldata[["ToySample"]]$tls_id_knn)
#> 
#>      0      1      2 
#> 321383   1115    453 
plot(ldata[["ToySample"]]$x, ldata[["ToySample"]]$y,
     col = ifelse(ldata[["ToySample"]]$tls_id_knn > 0, "red", "gray"),
     pch = 19, cex = 0.5, main = "Detected TLS in toy data")