# A function to create the color palette for the package
cite_colorPal <- function(n) {
cols_10 <- c("#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F",
"#EDC948", "#B07AA1", "#FF9DA7", "#9C755F", "#BAB0AC")
cols_20 <- c("#4E79A7", "#A0CBE8", "#F28E2B", "#FFBE7D", "#59A14F",
"#8CD17D", "#B6992D", "#F1CE63", "#499894", "#86BCB6",
"#E15759", "#FF9D9A", "#79706E", "#BAB0AC", "#D37295",
"#FABFD2", "#B07AA1", "#D4A6C8", "#9D7660", "#D7B5A6")
if (n <= length(cols_10)) {
return(cols_10[seq_len(n)])
} else if (n <= length(cols_20)) {
return(cols_20[seq_len(n)])
} else {
return(scales::gradient_n_pal(cols_20)(seq(0, 1, length.out = n)))
}
}
cite_shapePal <- function(n) {
return(c(16, 17, 15, 3, 6, 8, 1, 0, 5)[seq_len(n)])
}
#' @importFrom compositions clr
clr_rho <- function(counts){
# Adapting from the propr package
zeros <- counts == 0
counts[zeros] <- min(counts[!zeros])
# Calculate proportionality
lr <- compositions::clr(counts)
mat <- lr2rho(lr)
colnames(mat) <- colnames(counts)
rownames(mat) <- colnames(counts)
return(mat)
}
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