File size: 3,507 Bytes
9aaa76b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 | #' changeDendPartColor
#'
#' @param dendrogram dendrogram to modify
#' @param colorBy color by choosing number of groups, cut height, or metadata
#' @param colorBlindPalette colorblind palette
#' @param cutHeight height to cut dendrogram
#' @param chosenK number of groups for kmeans
#' @param part modify dendrogram's labels or lines
#'
#' @return modified dendrogram
#'
#'
changeDendPartColor <- function(dendrogram,
colorBy,
colorBlindPalette,
cutHeight = 0,
chosenK = 1,
part){
if(part == "branches" ){
dendFunc <- dendextend::color_branches
} else if (part == "labels") {
dendFunc <- dendextend::color_labels
}
wet <- dendrogram
if(class(dendrogram) != "dendrogram"){
warning("Dendrogram input wasn't of class \"dendrogram\"")
} else if (class(colorBy) != "character") {
warning(paste0("colorBy was type ", class(colorBy), ", expected character"))
} else if (class(colorBlindPalette) != "character") {
warning(paste0("colorBlindPalette was type ", class(colorBlindPalette), ", expected character vector."))
} else{
if(colorBy == "none") {
#Intentionally Blank
return(dendrogram)
} else if(colorBy == "height") {
req(cutHeight)
if(cutHeight > attributes(dendrogram)$height) {
cutHeight <- attributes(dendrogram)$height
}
if(cutHeight < 0){
cutHeight <- 0
}
dendrogram <- tryCatch(
dendFunc(dend = dendrogram,
h = cutHeight,
col = as.vector(colorBlindPalette[1:length(unique(dendextend::cutree(dendrogram, h = cutHeight)))])),
error = function(x) dendrogram,
finally = function(x) "Error when cutting dendrogram by height"
)
} else if(colorBy == "groups") {
req(chosenK)
if(is.na(chosenK)){
chosenK <- 1
}
if (chosenK > attributes(dendrogram)$members) {
chosenK <- attributes(dendrogram)$members
}
dendrogram <- tryCatch(
dendFunc(dend = dendrogram,
k = round(chosenK, digits = 0),
col = as.vector(colorBlindPalette[1:length(unique(dendextend::cutree(dendrogram, k = chosenK)))])),
error = function(x) "Error when cutting dendrogram by Kmeans"
)
} else if(colorBy == "metadata") {
return(
dendrogram
)
}
}
return(dendrogram)
}
#' changeDendPartSize
#'
#' @param dendrogram dendrogram to modify
#' @param dendPartSize numeric passed to change label size or edge widths
#' @param part change label size or edge widths
#'
#' @return modified dendrogram
#'
#'
changeDendPartSize <- function(dendrogram,
dendPartSize,
part){
if(part == "branches" ){
dendFunc <- "branches_lwd"
} else if (part == "labels") {
dendFunc <- "labels_cex"
}
if(class(dendrogram) != "dendrogram"){
warning("Dendrogram input wasn't of class \"dendrogram\"")
return(dendrogram)
} else if (!is.numeric(dendPartSize)) {
warning(base::paste0("size was type ", base::class(dendPartSize), ", expected numeric"))
return(dendrogram)
} else {
return(
dendextend::set(dendrogram, dendFunc, dendPartSize)
)
}
}
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