knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
In this article we will describe different ways to customise the appearance of an antigenic map with for example different point colours, shapes and sizes. We'll first describe the key functions and then go through an example.
The main functions for controlling point style parameters are:
agFill()
and srFill()
for controlling the antigen and sera fill colouragOutline()
and srOutline()
for controlling the antigen and sera outline colouragOutlineWidth()
and srOutlineWidth()
for controlling the antigen and sera outline stroke widthagSize()
and srSize()
for controlling the antigen and sera point sizesagShape()
and srShape()
for controlling the antigen and sera point shapesagShown()
and srShown()
for controlling whether antigen and serum points are visibleNote that the primary supported shapes values are "circle", "box" and "triangle", but see below for details on further map customisation.
There is also the function ptDrawingOrder()
which controls the order in which points are plotted according to their index in the map (numbering the antigens first then the sera).
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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