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/R/getMoHeatmap.R
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| a | b/R/getMoHeatmap.R | ||
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| 1 | #' @name getMoHeatmap |
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| 2 | #' @title Get multi-omics comprehensive heatmap |
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| 3 | #' @description This function vertically concatenates multiple heatmap derived from each omics data. `getMoHeatmap` supports customized column annotation and is able to mark the selected features if indicated. |
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| 4 | #' @param data A list of data frame or matrix storing multiple omics data with rows for features and columns for samples. |
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| 5 | #' @param is.binary A logicial vector to indicate if the subdata is binary matrix of 0 and 1 such as mutation. |
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| 6 | #' @param row.title A string vector to assign titles for each subdata. |
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| 7 | #' @param legend.name A string vector to assign legend title for each subdata. |
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| 8 | #' @param clust.res A clust.res object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms. |
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| 9 | #' @param clust.dend A dendrogram object returned returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms. |
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| 10 | #' @param show.col.dend A logical vector to indicate if showing the dendrogram for column at the top of heatmap. |
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| 11 | #' @param show.colnames A logical vector to indicate if showing the names for column at the bottom of heatmap. |
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| 12 | #' @param show.row.dend A logical vector to indicate if showing the dendrogram for row of each subdata. |
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| 13 | #' @param show.rownames A logical vector to indicate if showing the names for row of each subdata. |
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| 14 | #' @param clust.dist.row A string vector to assign distance method for clustering each subdata at feature dimension. |
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| 15 | #' @param clust.method.row A string vector to assign clustering method for clustering each subdata at feature dimension. |
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| 16 | #' @param clust.col A string vector storing colors for annotating each subtype at the top of heatmap. |
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| 17 | #' @param color A list of string vectors storing colors for each subheatmap of subdata. |
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| 18 | #' @param annCol A data.frame storing annotation information for samples with exact the same sample order with data parameter. |
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| 19 | #' @param annColors A list of string vectors for colors matched with annCol. |
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| 20 | #' @param annRow A list of string vectors to indicate which features belong to which subdata should be annotated specifically in subheatmap. |
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| 21 | #' @param width An integer value to indicate the width for each subheatmap with unit of cm. |
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| 22 | #' @param height An integer value to indicate the height for each subheatmap with unit of cm. |
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| 23 | #' @param fig.path A string value to indicate the output path for storing the comprehensive heatmap. |
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| 24 | #' @param fig.name A string value to indicate the name of the comprehensive heatmap. |
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| 25 | #' @return A pdf of multi-omics comprehensive heatmap |
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| 26 | #' @importFrom ComplexHeatmap HeatmapAnnotation Heatmap rowAnnotation anno_mark draw ht_opt %v% |
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| 27 | #' @importFrom ClassDiscovery distanceMatrix |
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| 28 | #' @importFrom grDevices pdf dev.off colorRampPalette |
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| 29 | #' @importFrom circlize colorRamp2 |
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| 30 | #' @importFrom dplyr %>% |
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| 31 | #' @references Gu Z, Eils R, Schlesner M (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. |
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| 32 | #' @export |
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| 33 | #' @examples # There is no example and please refer to vignette. |
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| 34 | getMoHeatmap <- function(data = NULL, |
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| 35 | is.binary = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE), |
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| 36 | row.title = c("Data1","Data2","Data3","Data4","Data5","Data6"), |
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| 37 | legend.name = c("Data1","Data2","Data3","Data4","Data5","Data6"), |
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| 38 | clust.res = NULL, |
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| 39 | clust.dend = NULL, |
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| 40 | show.col.dend = TRUE, |
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| 41 | show.colnames = FALSE, |
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| 42 | show.row.dend = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE), |
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| 43 | show.rownames = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE), |
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| 44 | clust.dist.row = c("pearson","pearson","pearson","pearson","pearson","pearson"), |
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| 45 | clust.method.row = c("ward.D","ward.D","ward.D","ward.D","ward.D","ward.D"), |
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| 46 | clust.col = c("#2EC4B6","#E71D36","#FF9F1C","#BDD5EA","#FFA5AB","#011627","#023E8A","#9D4EDD"), |
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| 47 | color = rep(list(c("#00FF00", "#000000", "#FF0000")),length(data)), |
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| 48 | annCol = NULL, |
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| 49 | annColors = NULL, |
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| 50 | annRow = NULL, |
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| 51 | width = 6, |
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| 52 | height = 4, |
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| 53 | fig.path = getwd(), |
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| 54 | fig.name = "moheatmap") { |
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| 55 | |||
| 56 | ht_opt$message = FALSE |
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| 57 | defaultW <- getOption("warn") |
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| 58 | options(warn = -1) |
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| 59 | |||
| 60 | # check data |
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| 61 | if(is.null(names(data))){ |
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| 62 | names(data) <- sprintf("dat%s", 1:length(data)) |
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| 63 | } |
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| 64 | |||
| 65 | n_dat <- length(data) |
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| 66 | if(n_dat > 6){ |
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| 67 | stop('current verision of MOVICS can support up to 6 datasets.') |
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| 68 | } |
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| 69 | if(n_dat < 2){ |
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| 70 | stop('current verision of MOVICS needs at least 2 omics data.') |
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| 71 | } |
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| 72 | |||
| 73 | colvec <- clust.col[1:length(unique(clust.res$clust))] |
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| 74 | names(colvec) <- paste0("CS",unique(clust.res$clust)) |
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| 75 | |||
| 76 | if(!is.null(annCol) & !is.null(annColors)) { |
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| 77 | |||
| 78 | annCol <- annCol[colnames(data[[1]]), , drop = FALSE] |
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| 79 | annCol$Subtype <- paste0("CS",clust.res[colnames(data[[1]]),"clust"]) |
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| 80 | annColors[["Subtype"]] <- colvec |
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| 81 | |||
| 82 | if(is.null(clust.dend)) { |
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| 83 | clust.res <- clust.res[order(clust.res$clust),] |
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| 84 | annCol <- annCol[clust.res$samID, , drop = FALSE] |
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| 85 | } |
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| 86 | |||
| 87 | ha <- ComplexHeatmap::HeatmapAnnotation(df = annCol, |
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| 88 | col = annColors, |
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| 89 | border = FALSE) |
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| 90 | } else { |
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| 91 | annCol <- data.frame("Subtype" = paste0("CS",clust.res[colnames(data[[1]]),"clust"]), |
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| 92 | row.names = colnames(data[[1]]), |
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| 93 | stringsAsFactors = FALSE) |
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| 94 | annColors <- list("Subtype" = colvec) |
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| 95 | |||
| 96 | if(is.null(clust.dend)) { |
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| 97 | clust.res <- clust.res[order(clust.res$clust),] |
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| 98 | annCol <- annCol[clust.res$samID,,drop = FALSE] |
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| 99 | } |
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| 100 | |||
| 101 | ha <- ComplexHeatmap::HeatmapAnnotation(df = annCol, |
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| 102 | col = annColors, |
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| 103 | border = FALSE) |
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| 104 | } |
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| 105 | |||
| 106 | if(!is.null(annRow)) { |
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| 107 | if(!is.list(annRow)) {stop("argument of annRow should be a list!")} |
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| 108 | } |
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| 109 | |||
| 110 | ht <- list() |
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| 111 | for (i in 1:n_dat) { |
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| 112 | |||
| 113 | hcg <- hclust(ClassDiscovery::distanceMatrix(as.matrix(t(data[[i]])), clust.dist.row[i]), clust.method.row[i]) |
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| 114 | |||
| 115 | if(is.null(annRow[[i]][1])) { |
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| 116 | rowlab <- "" |
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| 117 | rowlab.index <- 0 |
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| 118 | } else if (is.na(annRow[[i]][1])) { |
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| 119 | rowlab <- "" |
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| 120 | rowlab.index <- 0 |
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| 121 | } else { |
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| 122 | rowlab <- intersect(rownames(data[[i]]),annRow[[i]]) |
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| 123 | rowlab.index <- match(rowlab, rownames(data[[i]])) |
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| 124 | } |
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| 125 | |||
| 126 | if(is.null(clust.dend)) { |
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| 127 | data <- lapply(data, function(x) x[,clust.res$samID]) |
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| 128 | |||
| 129 | if(!is.binary[i]) { |
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| 130 | ht[[i]] <- ComplexHeatmap::Heatmap(matrix = as.matrix(data[[i]]), |
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| 131 | row_title = row.title[i], |
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| 132 | name = legend.name[i], |
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| 133 | cluster_columns = FALSE, |
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| 134 | cluster_rows = hcg, |
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| 135 | show_column_dend = FALSE, |
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| 136 | show_column_names = show.colnames, |
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| 137 | show_row_dend = show.row.dend[i], |
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| 138 | show_row_names = show.rownames[i], |
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| 139 | col = grDevices::colorRampPalette(color[[i]])(64), |
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| 140 | top_annotation = switch((i == 1) + 1, NULL, ha), |
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| 141 | width = grid::unit(width, "cm"), |
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| 142 | height = grid::unit(height, "cm"), |
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| 143 | heatmap_legend_param = list(at = pretty(range(data[[i]])), |
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| 144 | labels = pretty(range(data[[i]]))), |
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| 145 | right_annotation = ComplexHeatmap::rowAnnotation(link = |
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| 146 | anno_mark(at = rowlab.index, |
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| 147 | labels = rowlab, |
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| 148 | which = "row", |
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| 149 | lines_gp = grid::gpar(fontsize = 5), |
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| 150 | link_width = grid::unit(3, "mm"), |
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| 151 | padding = grid::unit(0.8, "mm"), |
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| 152 | labels_gp = grid::gpar(fontsize = 7)))) |
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| 153 | } else { |
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| 154 | col_fun = circlize::colorRamp2(c(0, 1), color[[i]]) |
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| 155 | |||
| 156 | ht[[i]] <- ComplexHeatmap::Heatmap(matrix = as.matrix(data[[i]]), |
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| 157 | row_title = row.title[i], |
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| 158 | name = legend.name[i], |
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| 159 | cluster_columns = FALSE, |
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| 160 | cluster_rows = hcg, |
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| 161 | show_column_dend = FALSE, |
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| 162 | show_column_names = show.colnames, |
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| 163 | show_row_dend = show.row.dend[i], |
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| 164 | show_row_names = show.rownames[i], |
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| 165 | col = color[[i]], |
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| 166 | top_annotation = switch((i == 1) + 1, NULL, ha), |
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| 167 | width = grid::unit(width, "cm"), |
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| 168 | height = grid::unit(height, "cm"), |
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| 169 | heatmap_legend_param = list(at = c(0, 1), |
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| 170 | legend_gp = grid::gpar(fill = col_fun(c(0,1))), |
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| 171 | labels = c("0", "1")), |
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| 172 | right_annotation = ComplexHeatmap::rowAnnotation(link = |
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| 173 | anno_mark(at = rowlab.index, |
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| 174 | labels = rowlab, |
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| 175 | which = "row", |
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| 176 | lines_gp = grid::gpar(fontsize = 5), |
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| 177 | link_width = grid::unit(3, "mm"), |
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| 178 | padding = grid::unit(0.8, "mm"), |
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| 179 | labels_gp = grid::gpar(fontsize = 7)))) |
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| 180 | } |
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| 181 | |||
| 182 | } else { |
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| 183 | if(!is.binary[i]) { |
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| 184 | ht[[i]] <- ComplexHeatmap::Heatmap(matrix = as.matrix(data[[i]]), |
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| 185 | row_title = row.title[i], |
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| 186 | name = legend.name[i], |
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| 187 | cluster_columns = clust.dend, |
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| 188 | cluster_rows = hcg, |
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| 189 | show_column_dend = show.col.dend, |
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| 190 | show_column_names = show.colnames, |
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| 191 | show_row_dend = show.row.dend[i], |
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| 192 | show_row_names = show.rownames[i], |
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| 193 | col = grDevices::colorRampPalette(color[[i]])(64), |
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| 194 | top_annotation = switch((i == 1) + 1, NULL, ha), |
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| 195 | width = grid::unit(width, "cm"), |
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| 196 | height = grid::unit(height, "cm"), |
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| 197 | heatmap_legend_param = list(at = pretty(range(data[[i]])), |
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| 198 | labels = pretty(range(data[[i]]))), |
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| 199 | right_annotation = ComplexHeatmap::rowAnnotation(link = |
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| 200 | anno_mark(at = rowlab.index, |
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| 201 | labels = rowlab, |
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| 202 | which = "row", |
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| 203 | lines_gp = grid::gpar(fontsize = 5), |
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| 204 | link_width = grid::unit(3, "mm"), |
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| 205 | padding = grid::unit(0.8, "mm"), |
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| 206 | labels_gp = grid::gpar(fontsize = 7)))) |
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| 207 | } else { |
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| 208 | col_fun = circlize::colorRamp2(c(0, 1), color[[i]]) |
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| 209 | |||
| 210 | ht[[i]] <- ComplexHeatmap::Heatmap(matrix = as.matrix(data[[i]]), |
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| 211 | row_title = row.title[i], |
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| 212 | name = legend.name[i], |
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| 213 | cluster_columns = clust.dend, |
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| 214 | cluster_rows = hcg, |
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| 215 | show_column_dend = show.col.dend, |
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| 216 | show_column_names = show.colnames, |
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| 217 | show_row_dend = show.row.dend[i], |
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| 218 | show_row_names = show.rownames[i], |
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| 219 | col = color[[i]], |
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| 220 | top_annotation = switch((i == 1) + 1, NULL, ha), |
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| 221 | width = grid::unit(width, "cm"), |
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| 222 | height = grid::unit(height, "cm"), |
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| 223 | heatmap_legend_param = list(at = c(0, 1), |
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| 224 | legend_gp = grid::gpar(fill = col_fun(c(0,1))), |
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| 225 | labels = c("0", "1")), |
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| 226 | right_annotation = ComplexHeatmap::rowAnnotation(link = |
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| 227 | anno_mark(at = rowlab.index, |
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| 228 | labels = rowlab, |
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| 229 | which = "row", |
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| 230 | lines_gp = grid::gpar(fontsize = 5), |
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| 231 | link_width = grid::unit(3, "mm"), |
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| 232 | padding = grid::unit(0.8, "mm"), |
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| 233 | labels_gp = grid::gpar(fontsize = 7)))) |
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| 234 | } |
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| 235 | } |
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| 236 | } |
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| 237 | |||
| 238 | if(n_dat == 1){ |
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| 239 | ht_list <- ht[[1]] |
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| 240 | } |
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| 241 | if(n_dat == 2){ |
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| 242 | ht_list <- ht[[1]] %v% ht[[2]] |
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| 243 | } |
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| 244 | if(n_dat == 3){ |
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| 245 | ht_list <- ht[[1]] %v% ht[[2]] %v% ht[[3]] |
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| 246 | } |
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| 247 | if(n_dat == 4){ |
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| 248 | ht_list <- ht[[1]] %v% ht[[2]] %v% ht[[3]] %v% ht[[4]] |
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| 249 | } |
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| 250 | if(n_dat == 5){ |
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| 251 | ht_list <- ht[[1]] %v% ht[[2]] %v% ht[[3]] %v% ht[[4]] %v% ht[[5]] |
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| 252 | } |
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| 253 | if(n_dat == 6){ |
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| 254 | ht_list <- ht[[1]] %v% ht[[2]] %v% ht[[3]] %v% ht[[4]] %v% ht[[5]] %v% ht[[6]] |
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| 255 | } |
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| 256 | |||
| 257 | outFile <- file.path(fig.path,paste0(fig.name,".pdf")) |
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| 258 | if(is.null(annCol)) { |
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| 259 | pdf(outFile, width = width, height = height * n_dat/2) |
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| 260 | } else { |
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| 261 | pdf(outFile, width = width, height = height * n_dat/1.5) |
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| 262 | } |
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| 263 | draw(ht_list, merge_legend = TRUE, heatmap_legend_side = "right") # output to pdf |
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| 264 | invisible(dev.off()) |
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| 265 | |||
| 266 | draw(ht_list, merge_legend = TRUE, heatmap_legend_side = "right") # output to screen |
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| 267 | |||
| 268 | options(warn = defaultW) |
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| 269 | } |