R/utils.R

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

# 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)
}