Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
eval = rmarkdown::pandoc_available()
)
## ----add_sequences------------------------------------------------------------
library(Racmacs)
# Load the h3 antigenic map
map <- read.acmap(system.file("extdata/h3map2004.ace", package = "Racmacs"))
# Load the antigen and serum sequence data
ag_sequences <- read.csv(
file = system.file("extdata/h3map2004_sequences_ag.csv", package = "Racmacs"),
colClasses = "character",
row.names = 1
)
sr_sequences <- read.csv(
file = system.file("extdata/h3map2004_sequences_sr.csv", package = "Racmacs"),
colClasses = "character",
row.names = 1
)
# Add the sequence data to the map
agSequences(map) <- ag_sequences
srSequences(map) <- sr_sequences
## ----view_map, out.width="100%"-----------------------------------------------
# View the map with sequence data
view(map)
## ----view_seq_coloring, out.width="100%", out.height="600px", echo=FALSE------
view(
map,
.jsCode = "function(el, x, data) {
el.viewer.showControlPanel();
el.viewer.openControlTab('colorpanel');
el.viewer.colorBySequenceAtPosition(145);
}"
)
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