Plot a lineage definition matrix

Usage

plot_lineage_defs(
  lineage_defs,
  col = colorRampPalette(colors = c("white", "dodgerblue4")),
  main = NULL
)

Arguments

lineage_defs: Lineage definition matrix, such as those produced by astronomize() and usher_barcodes().Alternatively the output of provoc(), from which the lineage definition matrix will be extracted.
col: A function that takes argument n and returns a vector of colours of length n, such as colorRampPallette(c("white", "dodgerblue4"))
main: a main title for the plot.

Details

Every second column in the display has a slight grey background to make it easier to read which mutation is in which lineage.

The final column summarises the number of mutations that are unique to a given variant, with the darker colour representing a variant with more unique mutations. The number in the brackets gives the exact number of unique mutations.

Examples

# Choose lineages that I know have a lot of shared mutations
lineage_defs <- astronomize() |>
    filter_lineages(c("B.1.1.7", "B.1.617.1", "B.1.617.2",
        "B.1.617.2+K417N", "B.1.617.3", "XBB.1"))
# XBB.1 has 1 shared mutation and 2 unique mutations
# None of B.1.1.7's mutations are shared
plot_lineage_defs(lineage_defs)