Plot Spatial Map of TLS and T-cell Clusters

Produces a ggplot2 scatter plot of cell positions, coloured by TLS membership, T-cell cluster membership, and background phenotype.

Background (non-TLS, non-TIC) cells are rendered with a lower alpha to keep them visually recessive, while TIC cells are drawn slightly larger than TLS cells so they stand out without dominating the plot.

Usage

plot_TLS(
  sample,
  ldata = NULL,
  show_tic = TRUE,
  point_size = 0.5,
  alpha = 0.7,
  bg_alpha = 0.25,
  tic_size_mult = 1.8,
  tls_palette = c("#0072B2", "#009E73", "#CC79A7", "#D55E00", "#56B4E9", "#F0E442"),
  tic_colour = "#E69F00",
  bg_colour = "grey80"
)

Arguments

sample

Character. Sample name in ldata.

ldata

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

show_tic

Logical. Colour T-cell clusters (if detect_tic has been run) in a distinct colour? Default TRUE.

point_size

Numeric. Base point size for TLS cells and background cells (default 0.5). TIC cells are drawn at point_size * tic_size_mult.

alpha

Numeric. Point transparency for TLS and TIC cells (default 0.7).

bg_alpha

Numeric. Point transparency for background (non-TLS, non-TIC) cells (default 0.25). Reducing this value pushes background cells further behind the foreground structure.

tic_size_mult

Numeric. Multiplier applied to point_size for TIC cells so they appear slightly larger than background and TLS cells (default 1.8).

tls_palette

Character vector of colours for TLS IDs. Recycled if there are more TLS than colours. Default uses a colourblind-friendly palette.

tic_colour

Character. Colour for T-cell cluster cells (default "#E69F00").

bg_colour

Character. Colour for non-TLS, non-TIC cells (default "grey80").

Value

A ggplot object (invisibly). The plot is also printed unless the return value is assigned.

Examples

data(toy_ldata)
ldata <- detect_TLS("ToySample", k = 30, ldata = toy_ldata)
#> Detected TLS: 2
# \donttest{
  p <- plot_TLS("ToySample", ldata = ldata)
# }