Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## -----------------------------------------------------------------------------
library(Racmacs)
map <- read.acmap(system.file("extdata/h3map2004.ace", package = "Racmacs"))
# Rotate the map
map <- rotateMap(map, 210)
# Colour all the antigens grey
agFill(map) <- "grey50"
# Colour all the vaccine antigens in red and increase their size
vaccine_strains <- c(
"PC/1/73",
"VI/3/75",
"TE/1/77",
"BA/1/79",
"PH/2/82",
"LE/360/86",
"SH/11/87",
"SI/2/87",
"BE/353/89",
"GU/54/89",
"BE/32/92",
"SD/9/93",
"JO/33/94",
"WU/359/95",
"SY/5/97",
"MW/10/99",
"FU/411/02"
)
vaccine_ags <- agNames(map) %in% vaccine_strains
agFill(map)[vaccine_ags] <- "red"
agSize(map)[vaccine_ags] <- 8
# Bring the antigens to the top of the plot
ptDrawingOrder(map) <- c(
seq_len(numSera(map)) + numAntigens(map), # Draw sera first
which(!vaccine_ags), # Then draw non vaccine ags
which(vaccine_ags) # The draw vaccine ags
)
# Plot the map
plot(map)
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