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Plot a TCR clone network

Source: R/network.R
plot_tcr_network.Rd

Draws a network graph of TCR clones with ggplot2, using layout coordinates from compute_tcr_network. Vertices are colored by a metadata variable (e.g. epitope, cluster) and edges are drawn as semi-transparent segments.

Usage

plot_tcr_network(
  network,
  color_by = NULL,
  vertex_size = 3,
  edge_alpha = 0.15,
  edge_width = 0.3,
  title = NULL,
  palette = NULL,
  legend_title = NULL,
  show_labels = FALSE,
  label_size = 3,
  na_color = "#DDDDDD"
)

Arguments

network

List returned by compute_tcr_network.

color_by

Character string naming a vertex attribute, OR a vector of length N. If a single string matching a vertex attribute name, that attribute is used. If NULL, all vertices are gray.

vertex_size

Numeric. Point size. Default 3.

edge_alpha

Numeric. Edge transparency. Default 0.15.

edge_width

Numeric. Edge line width. Default 0.3.

title

Optional plot title.

palette

Character vector of colors to override the default palette.

legend_title

Optional legend title.

show_labels

Logical. If TRUE and coloring is categorical, add centroid labels. Default FALSE.

label_size

Numeric. Label text size. Default 3.

na_color

Character. Color for NA values. Default "#DDDDDD".

Value

A ggplot object.

See also

compute_tcr_network, plot_tcr_scatter

Examples

# \donttest{
data(dash)
sub <- dash[1:200, ]
net <- compute_tcr_network(sub, "mouse", threshold = 48, seed = 42)

plot_tcr_network(net, color_by = "epitope", title = "TCR network")

# }