inst/seg-stuff/oncoprint.R
In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data
#'
#' #' Creates the OncoPrint corresponding to the inputted genetic data
#' #' @param gen_dat A binary matrix or dataframe, with samples as rows and features as columns. Note that the names of the
#' #' columns must end in ".Del" or ".Amp" to recognize copy number alterations. (see create.bin.matrix for more details on this format).
#' #' @param clin_dat An optional clinical file, including only the features the user wishes to add to the plot. Default is NULL.
#' #' @param ordered_samples An optional vector of length equal to the number of samples under consideration. Indicates the new order (from left to right)
#' #' to be plotted.
#' #' @param rank_genes Boolean argument specifying if the genes should be ranked by event frequency. Default is TRUE.
#' #' @param background_color Color name to be used to fill the background of the OncoPrint.
#' #' @return an oncoprint object
#' #' @export
#' #' @examples library(gnomeR)
#' #' @import
#' #' ComplexHeatmap
#' #' tibble
#'
#' plot_oncoprint <- function(gen_dat,
#' clin_dat=NULL,
#' ordered_samples=NULL,
#' rank_genes = TRUE,
#' background_color = "#CCCCCC"){
#'
#'
#' # if(rank_genes){
#' oncoprint_column_order = function(count_matrix = NULL) {
#' scoreCol = function(x) {
#' score = 0
#' for (i in 1:length(x)) {
#' if (x[i]) {
#' score = score + 2^(length(x) - i * 1/x[i])
#' }
#' }
#' return(score)
#' }
#' scores = apply(count_matrix[row_order, , drop = FALSE],
#' 2, scoreCol)
#' order(scores, decreasing = TRUE)
#' }
#' # }
#' # else{
#' # oncoprint_column_order <- function(count_matrix = NULL){
#' # 1:ncol(count_matrix)
#' # }
#' # }
#'
#'
#' # make data #
#' mat <- dat_oncoprint(gen_dat,clin_dat)
#' #############
#' if(!is.null(clin_dat)){
#' # get all values #
#' clin.factors <- unique(unlist(apply(mat,2,unique)))
#' clin.factors <- clin.factors[-stats::na.omit(match(c("MUT;","AMP;","DEL;","FUS;"," ","MIS;",
#' "MUT;FUS;","MUT;DEL;","MUT;AMP;","MUT;DEL;FUS;",
#' "DEL;FUS;","MUT;AMP;FUS;",
#' "AMP;FUS;"),clin.factors))]
#' if(length(clin.factors) == 0){
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange","MIS" = "black")
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' to.add <- NULL
#' added <- NULL
#' }
#'
#' if(length(clin.factors) > 0){
#' clin.factors <- gsub(";","",clin.factors)
#' sum.factors <- summary(as.factor(gsub("_.*","",clin.factors)))
#' added <- c()
#' names.toadd <- c()
#'
#' for(k in 1:length(sum.factors)){
#' if(as.numeric(sum.factors[k]) == 2){
#' added <- c(added, c("purple", background_color))
#' names.toadd <- c(names.toadd,
#' levels(as.factor(clin.factors[grep(names(sum.factors)[k],clin.factors)])))
#' }
#' else{
#' added <- c(added, grDevices::palette()[c(3,7,2,6,5,4,1)][1:as.numeric(sum.factors[k])])
#'
#' names.toadd <- c(names.toadd,
#' levels(as.factor(clin.factors[grep(names(sum.factors)[k],clin.factors)])))
#' }
#' }
#' names(added) <- names.toadd
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange","MIS" = "black",added)
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' to.add <- lapply(as.character(added),function(val){
#' temp <- function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = val, col = NA))
#' }
#' })
#' names(to.add) <- names(added)
#' alter_fun <- c(alter_fun,to.add)
#' }
#'
#' if(!is.null(ordered_samples)) {
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' sorted.mat <- mat[row_order,ordered_samples]
#'
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS",names(added)),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing",names(added))),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' else{
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' get_type2 = function(x) gsub("^\\s+|\\s+$", "", ComplexHeatmap::default_get_type(x))
#' all_type = unique(unlist(lapply(mat, get_type2)))
#' all_type = all_type[!is.na(all_type)]
#' all_type = all_type[grepl("\\S", all_type)]
#' mat_list = lapply(all_type, function(type) {
#' m = sapply(mat, function(x) type %in% get_type2(x))
#' dim(m) = dim(mat)
#' dimnames(m) = dimnames(mat)
#' m
#' })
#' names(mat_list) = all_type[grep("MUT|DEL|AMP|FUS",all_type)]
#'
#' arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)),
#' dimnames = c(dimnames(mat_list[[1]]), list(all_type)))
#' for (i in seq_along(all_type)) {
#' arr[, , i] = mat_list[[i]]
#' }
#' count_matrix = apply(arr, c(1, 2), sum)
#'
#' column_order = oncoprint_column_order(count_matrix = count_matrix)
#'
#' sorted.mat <- mat[row_order,column_order]
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS",names(added)),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing",names(added))),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' }
#'
#'
#' if(is.null(clin_dat)){
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange", "MIS" = "black")
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' if(!is.null(ordered_samples)) {
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' sorted.mat <- mat[row_order,ordered_samples]
#'
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS"),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing")),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' else{
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' get_type2 = function(x) gsub("^\\s+|\\s+$", "", ComplexHeatmap::default_get_type(x))
#' all_type = unique(unlist(lapply(mat, get_type2)))
#' all_type = all_type[!is.na(all_type)]
#' all_type = all_type[grepl("\\S", all_type)]
#' mat_list = lapply(all_type, function(type) {
#' m = sapply(mat, function(x) type %in% get_type2(x))
#' dim(m) = dim(mat)
#' dimnames(m) = dimnames(mat)
#' m
#' })
#' names(mat_list) = all_type[-match("MIS",all_type)]
#'
#' arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)),
#' dimnames = c(dimnames(mat_list[[1]]), list(all_type)))
#' for (i in seq_along(all_type)) {
#' arr[, , i] = mat_list[[i]]
#' }
#' count_matrix = apply(arr, c(1, 2), sum)
#'
#' column_order = oncoprint_column_order(count_matrix = count_matrix)
#'
#'
#' sorted.mat <- mat[row_order,column_order]
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS"),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing")),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' }
#'
#' return(p)
#' }
#'
#'
#'
#' #' Enables creation of a matrix used to generate an OncoPrint heatmap.
#' #' @param gen_dat A binary matrix or dataframe, with samples as rows and features as columns. Note that the names of the
#' #' columns must end in ".Del" or ".Amp" to recognize copy number alterations. (see create.bin.matrix for more details on this format).
#' #' @param clin_dat An optional clinical file, including only the features the user wishes to add to the plot. Default is NULL.
#' #' @return mat : a matrix ready to be plotted using plot.OncoPrint().
#' #' @export
#' #' @examples
#' #' library(gnomeR)
#' #' library(dplyr)
#' #' samples <- as.character(unique(gnomeR::mutations))
#' #' bin.mut <- create_gene_binary(samples = samples, mutation = gnomeR::mutations,
#' #' mut_type = "somatic_only",
#' #' snp_only = FALSE, include_silent = FALSE, specify_panel = "no")
#' #' gen_dat <- bin.mut[1:500,names(sort(apply(bin.mut,2, sum), decreasing = TRUE))[1:15]]
#' #' dat <- dat_oncoprint(gen_dat)
#' #'
#' #' ## adding clinical ##
#' #' clin.patients.dat <-
#' #' clin.patients[match(abbreviate(rownames(gen_dat),
#' #' strict = TRUE, minlength = 9),
#' #' clin.patients$X.Patient.Identifier),] %>%
#' #' dplyr::rename(DMPID = X.Patient.Identifier,
#' #' Smoker = Smoking.History) %>%
#' #' dplyr::select(DMPID, Sex,Smoker) %>%
#' #' dplyr::filter(!is.na(DMPID)) %>%
#' #' dplyr::distinct(DMPID,.keep_all = TRUE)
#' #' gen_dat <- gen_dat[match(clin.patients.dat$DMPID,
#' #' abbreviate(rownames(gen_dat),strict = TRUE, minlength = 9)),]
#' #' clin.patients.dat <- clin.patients.dat %>%
#' #' dplyr::mutate(DMPID = as.character(DMPID)) %>%
#' #' tibble::rownames_to_column("to_rm") %>%
#' #' select(-one_of("to_rm")) %>%
#' #' tibble::column_to_rownames('DMPID')
#' #' rownames(gen_dat) <- rownames(clin.patients.dat)
#' #' dat <- dat_oncoprint(gen_dat = gen_dat, clin_dat = clin.patients.dat)
#' #' @import
#' #' tibble
#' #' dplyr
#'
#'
#' dat_oncoprint <- function(gen_dat, clin_dat=NULL){
#'
#' # would be best if genetics also had an unknown #
#' # if(anyNA(gen_dat))
#' # gen_dat[is.na(gen_dat)] <- 0
#'
#' # check if data has non binary cna data and fix it #
#' if(length(grep(".cna", colnames(gen_dat))) > 0){
#' temp <- gen_dat[,grep(".cna",colnames(gen_dat))]
#'
#' temp2 <- do.call("cbind",apply(temp,2,function(x){
#' x <- as.numeric(as.character(x))
#' yA <- ifelse(x>=0.9,1,0)
#' yD <- ifelse(x<=-0.9,1,0)
#' out <- as.data.frame(cbind(yA,yD))
#' colnames(out) <- c("Amp","Del")
#' return(out)
#' }))
#' colnames(temp2) <- gsub("\\.cna","",colnames(temp2))
#' gen_dat <- as.data.frame(cbind(gen_dat[,-grep(".cna",colnames(gen_dat))],
#' temp2))
#' }
#'
#' # check that gen_dat is a binary matrix #
#' if(anyNA(apply(gen_dat, 2, function(x){anyNA(as.numeric(x[!is.na(x)]))}))){
#' warning("All genetic components were not numeric. Those which weren't will be removed")
#' gen_dat <- gen_dat[,-which(apply(gen_dat,2,function(x){anyNA(as.numeric(x[!is.na(x)]))}))]
#' }
#'
#' if(!all(apply(gen_dat,2,function(x){length(unique(x[!is.na(x)])) <= 2}))){
#' warning("All genetic components were not binary. Those which weren't will be removed")
#' gen_dat <- gen_dat[,-which(apply(gen_dat,2,function(x){length(unique(x[!is.na(x)])) > 2}))]
#' }
#'
#'
#' if(!is.null(clin_dat)){
#' # seet NA's to UNKNOWN #
#' clin_dat <- clin_dat %>%
#' tibble::rownames_to_column('sample') %>%
#' mutate_all(as.character) %>%
#' tibble::column_to_rownames('sample')
#' if(anyNA(clin_dat)) clin_dat[is.na(clin_dat)] <- "Unknown"
#' # subset data #
#' patients <- intersect(rownames(gen_dat),rownames(clin_dat))
#' gen_dat <- gen_dat[match(patients,rownames(gen_dat)),]
#' clin_dat <- clin_dat %>%
#' tibble::rownames_to_column('sample')
#' clin_dat <- clin_dat[match(patients,clin_dat$sample),]
#' rownames(clin_dat) <- clin_dat$sample
#' clin_dat <- clin_dat %>%
#' select(-one_of("sample"))
#' ## names ##
#' genes <- c(colnames(clin_dat),unique(gsub(".Amp|.Del|.fus","",colnames(gen_dat))))
#' }
#' else genes <- unique(gsub(".Amp|.Del|.fus","",colnames(gen_dat)))
#'
#' mat <- as.data.frame(matrix(nrow=length(genes),ncol=nrow(gen_dat)))
#' colnames(mat) <- rownames(gen_dat)
#' rownames(mat) <- genes
#'
#' # mutations #
#' mut <- gen_dat[,stats::na.omit(match(genes,colnames(gen_dat)))]
#'
#' for(i in 1:nrow(mut)){
#' for(j in 1:ncol(mut)){
#' if(!is.na(mut[i,j])){
#' if(mut[i,j]==1) {
#' mat[match(colnames(mut)[j],rownames(mat)),match(rownames(mut)[i],colnames(mat))] <- "MUT;"
#' }
#' }
#' else{
#' mat[match(colnames(mut)[j],rownames(mat)),match(rownames(mut)[i],colnames(mat))] <- "MIS;"
#' }
#' }
#' }
#'
#' # del #
#' if(length(stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))) > 0){
#' del <- gen_dat[,stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))]
#' if(is.null(dim(del))) {
#' del <- as.data.frame(del)
#' rownames(del) <- rownames(gen_dat)
#' }
#' colnames(del) <- gsub(".Del","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))])
#' for(i in 1:nrow(del)){
#' for(j in 1:ncol(del)){
#' if(!is.na(del[i,j])){
#' if(del[i,j]==1) {
#' if(!is.na(mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))])){
#' mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))],"DEL;")}
#' else{mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))] <- "DEL;"}
#' }
#' }
#' }
#' }
#' }
#'
#' # amp #
#' if(length(stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))) > 0){
#' amp <- gen_dat[,stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))]
#' if(is.null(dim(amp))) {
#' amp <- as.data.frame(amp)
#' rownames(amp) <- rownames(gen_dat)
#' }
#' colnames(amp) <- gsub(".Amp","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))])
#' for(i in 1:nrow(amp)){
#' for(j in 1:ncol(amp)){
#' if(!is.na(amp[i,j])){
#' if(amp[i,j]==1) {
#' if(!is.na(mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))])){
#' mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))],"AMP;")}
#' else{mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))] <- "AMP;"}
#' }
#' }
#' }
#' }
#' }
#'
#' # fusions #
#' if(length(stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))) > 0){
#' fusion <- gen_dat[,stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))]
#' if(is.null(dim(fusion))) {
#' fusion <- as.data.frame(fusion)
#' rownames(fusion) <- rownames(gen_dat)
#' }
#' colnames(fusion) <- gsub(".fus","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))])
#' for(i in 1:nrow(fusion)){
#' for(j in 1:ncol(fusion)){
#' if(!is.na(fusion[i,j])){
#' if(fusion[i,j]==1) {
#' if(!is.na(mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))])){
#' mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))],"FUS;")}
#' else{mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))] <- "FUS;"}
#' }
#' }
#' }
#' }
#' }
#' ### clin ###
#' if(!is.null(clin_dat)){
#' temp <- clin_dat
#' for(x in colnames(clin_dat)){
#' y <- clin_dat[,x]
#'
#' # if binary #
#' if(length(unique(y[!is.na(y)])) == 2){
#' mat[match(x,rownames(mat)),] <- paste0(x,"_",y,";") #ifelse(y==1,"CLIN;",NA)
#' }
#'
#' else if(length(unique(y[!is.na(y)])) %in% c(3:5)){
#' mat[match(x,rownames(mat)),] <- paste0(x,"_",y,";") #abbreviate(x,1)
#' }
#'
#' else{
#' y <- as.numeric(y)
#' mat[match(x,rownames(mat)),] <- ifelse(y > stats::median(y,na.rm = T),paste0(x,";"),NA)
#' }
#' }
#' }
#' ###
#' mat[is.na(mat)] <- " "
#' mat <- as.matrix(mat)
#'
#' return(mat)
#' }
#'
#'
MSKCC-Epi-Bio/gnomeR documentation built on March 28, 2024, 2:42 a.m.
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#'
#' #' Creates the OncoPrint corresponding to the inputted genetic data
#' #' @param gen_dat A binary matrix or dataframe, with samples as rows and features as columns. Note that the names of the
#' #' columns must end in ".Del" or ".Amp" to recognize copy number alterations. (see create.bin.matrix for more details on this format).
#' #' @param clin_dat An optional clinical file, including only the features the user wishes to add to the plot. Default is NULL.
#' #' @param ordered_samples An optional vector of length equal to the number of samples under consideration. Indicates the new order (from left to right)
#' #' to be plotted.
#' #' @param rank_genes Boolean argument specifying if the genes should be ranked by event frequency. Default is TRUE.
#' #' @param background_color Color name to be used to fill the background of the OncoPrint.
#' #' @return an oncoprint object
#' #' @export
#' #' @examples library(gnomeR)
#' #' @import
#' #' ComplexHeatmap
#' #' tibble
#'
#' plot_oncoprint <- function(gen_dat,
#' clin_dat=NULL,
#' ordered_samples=NULL,
#' rank_genes = TRUE,
#' background_color = "#CCCCCC"){
#'
#'
#' # if(rank_genes){
#' oncoprint_column_order = function(count_matrix = NULL) {
#' scoreCol = function(x) {
#' score = 0
#' for (i in 1:length(x)) {
#' if (x[i]) {
#' score = score + 2^(length(x) - i * 1/x[i])
#' }
#' }
#' return(score)
#' }
#' scores = apply(count_matrix[row_order, , drop = FALSE],
#' 2, scoreCol)
#' order(scores, decreasing = TRUE)
#' }
#' # }
#' # else{
#' # oncoprint_column_order <- function(count_matrix = NULL){
#' # 1:ncol(count_matrix)
#' # }
#' # }
#'
#'
#' # make data #
#' mat <- dat_oncoprint(gen_dat,clin_dat)
#' #############
#' if(!is.null(clin_dat)){
#' # get all values #
#' clin.factors <- unique(unlist(apply(mat,2,unique)))
#' clin.factors <- clin.factors[-stats::na.omit(match(c("MUT;","AMP;","DEL;","FUS;"," ","MIS;",
#' "MUT;FUS;","MUT;DEL;","MUT;AMP;","MUT;DEL;FUS;",
#' "DEL;FUS;","MUT;AMP;FUS;",
#' "AMP;FUS;"),clin.factors))]
#' if(length(clin.factors) == 0){
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange","MIS" = "black")
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' to.add <- NULL
#' added <- NULL
#' }
#'
#' if(length(clin.factors) > 0){
#' clin.factors <- gsub(";","",clin.factors)
#' sum.factors <- summary(as.factor(gsub("_.*","",clin.factors)))
#' added <- c()
#' names.toadd <- c()
#'
#' for(k in 1:length(sum.factors)){
#' if(as.numeric(sum.factors[k]) == 2){
#' added <- c(added, c("purple", background_color))
#' names.toadd <- c(names.toadd,
#' levels(as.factor(clin.factors[grep(names(sum.factors)[k],clin.factors)])))
#' }
#' else{
#' added <- c(added, grDevices::palette()[c(3,7,2,6,5,4,1)][1:as.numeric(sum.factors[k])])
#'
#' names.toadd <- c(names.toadd,
#' levels(as.factor(clin.factors[grep(names(sum.factors)[k],clin.factors)])))
#' }
#' }
#' names(added) <- names.toadd
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange","MIS" = "black",added)
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' to.add <- lapply(as.character(added),function(val){
#' temp <- function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = val, col = NA))
#' }
#' })
#' names(to.add) <- names(added)
#' alter_fun <- c(alter_fun,to.add)
#' }
#'
#' if(!is.null(ordered_samples)) {
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' sorted.mat <- mat[row_order,ordered_samples]
#'
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS",names(added)),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing",names(added))),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' else{
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' get_type2 = function(x) gsub("^\\s+|\\s+$", "", ComplexHeatmap::default_get_type(x))
#' all_type = unique(unlist(lapply(mat, get_type2)))
#' all_type = all_type[!is.na(all_type)]
#' all_type = all_type[grepl("\\S", all_type)]
#' mat_list = lapply(all_type, function(type) {
#' m = sapply(mat, function(x) type %in% get_type2(x))
#' dim(m) = dim(mat)
#' dimnames(m) = dimnames(mat)
#' m
#' })
#' names(mat_list) = all_type[grep("MUT|DEL|AMP|FUS",all_type)]
#'
#' arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)),
#' dimnames = c(dimnames(mat_list[[1]]), list(all_type)))
#' for (i in seq_along(all_type)) {
#' arr[, , i] = mat_list[[i]]
#' }
#' count_matrix = apply(arr, c(1, 2), sum)
#'
#' column_order = oncoprint_column_order(count_matrix = count_matrix)
#'
#' sorted.mat <- mat[row_order,column_order]
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS",names(added)),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing",names(added))),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' }
#'
#'
#' if(is.null(clin_dat)){
#' col = c("MUT" = "#008000", "AMP" = "red", "DEL" = "blue", "FUS" = "orange", "MIS" = "black")
#' alter_fun = list(
#' background = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = background_color, col = NA))
#' },
#' DEL = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "blue", col = NA))
#' },
#' AMP = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = grid::gpar(fill = "red", col = NA))
#' },
#' MUT = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "#008000", col = NA))
#' },
#' FUS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "orange", col = NA))
#' },
#' MIS = function(x, y, w, h) {
#' grid::grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = grid::gpar(fill = "black", col = NA))
#' }
#' )
#'
#' if(!is.null(ordered_samples)) {
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' sorted.mat <- mat[row_order,ordered_samples]
#'
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS"),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing")),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' else{
#' if(rank_genes)
#' row_order <- order(apply(mat, 1, function(x){sum(gsub("MIS;"," ",x) != " ")}),decreasing = T)
#' else
#' row_order <- 1:nrow(mat)
#'
#' get_type2 = function(x) gsub("^\\s+|\\s+$", "", ComplexHeatmap::default_get_type(x))
#' all_type = unique(unlist(lapply(mat, get_type2)))
#' all_type = all_type[!is.na(all_type)]
#' all_type = all_type[grepl("\\S", all_type)]
#' mat_list = lapply(all_type, function(type) {
#' m = sapply(mat, function(x) type %in% get_type2(x))
#' dim(m) = dim(mat)
#' dimnames(m) = dimnames(mat)
#' m
#' })
#' names(mat_list) = all_type[-match("MIS",all_type)]
#'
#' arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)),
#' dimnames = c(dimnames(mat_list[[1]]), list(all_type)))
#' for (i in seq_along(all_type)) {
#' arr[, , i] = mat_list[[i]]
#' }
#' count_matrix = apply(arr, c(1, 2), sum)
#'
#' column_order = oncoprint_column_order(count_matrix = count_matrix)
#'
#'
#' sorted.mat <- mat[row_order,column_order]
#' p <- oncoPrint(sorted.mat, get_type = function(x) strsplit(x, ";")[[1]],
#' alter_fun = alter_fun, col = col, column_order = 1:ncol(sorted.mat),row_order = 1:nrow(sorted.mat),
#' heatmap_legend_param = list(title = "Alterations", at = c("MUT","DEL","AMP","FUS","MIS"),
#' labels = c("Mutation","Deletion","Amplification","Fusion","Missing")),
#' top_annotation = HeatmapAnnotation(
#' column_barplot = anno_oncoprint_barplot(c("MUT","DEL","AMP","FUS"))),
#' alter_fun_is_vectorized = FALSE)
#' }
#' }
#'
#' return(p)
#' }
#'
#'
#'
#' #' Enables creation of a matrix used to generate an OncoPrint heatmap.
#' #' @param gen_dat A binary matrix or dataframe, with samples as rows and features as columns. Note that the names of the
#' #' columns must end in ".Del" or ".Amp" to recognize copy number alterations. (see create.bin.matrix for more details on this format).
#' #' @param clin_dat An optional clinical file, including only the features the user wishes to add to the plot. Default is NULL.
#' #' @return mat : a matrix ready to be plotted using plot.OncoPrint().
#' #' @export
#' #' @examples
#' #' library(gnomeR)
#' #' library(dplyr)
#' #' samples <- as.character(unique(gnomeR::mutations))
#' #' bin.mut <- create_gene_binary(samples = samples, mutation = gnomeR::mutations,
#' #' mut_type = "somatic_only",
#' #' snp_only = FALSE, include_silent = FALSE, specify_panel = "no")
#' #' gen_dat <- bin.mut[1:500,names(sort(apply(bin.mut,2, sum), decreasing = TRUE))[1:15]]
#' #' dat <- dat_oncoprint(gen_dat)
#' #'
#' #' ## adding clinical ##
#' #' clin.patients.dat <-
#' #' clin.patients[match(abbreviate(rownames(gen_dat),
#' #' strict = TRUE, minlength = 9),
#' #' clin.patients$X.Patient.Identifier),] %>%
#' #' dplyr::rename(DMPID = X.Patient.Identifier,
#' #' Smoker = Smoking.History) %>%
#' #' dplyr::select(DMPID, Sex,Smoker) %>%
#' #' dplyr::filter(!is.na(DMPID)) %>%
#' #' dplyr::distinct(DMPID,.keep_all = TRUE)
#' #' gen_dat <- gen_dat[match(clin.patients.dat$DMPID,
#' #' abbreviate(rownames(gen_dat),strict = TRUE, minlength = 9)),]
#' #' clin.patients.dat <- clin.patients.dat %>%
#' #' dplyr::mutate(DMPID = as.character(DMPID)) %>%
#' #' tibble::rownames_to_column("to_rm") %>%
#' #' select(-one_of("to_rm")) %>%
#' #' tibble::column_to_rownames('DMPID')
#' #' rownames(gen_dat) <- rownames(clin.patients.dat)
#' #' dat <- dat_oncoprint(gen_dat = gen_dat, clin_dat = clin.patients.dat)
#' #' @import
#' #' tibble
#' #' dplyr
#'
#'
#' dat_oncoprint <- function(gen_dat, clin_dat=NULL){
#'
#' # would be best if genetics also had an unknown #
#' # if(anyNA(gen_dat))
#' # gen_dat[is.na(gen_dat)] <- 0
#'
#' # check if data has non binary cna data and fix it #
#' if(length(grep(".cna", colnames(gen_dat))) > 0){
#' temp <- gen_dat[,grep(".cna",colnames(gen_dat))]
#'
#' temp2 <- do.call("cbind",apply(temp,2,function(x){
#' x <- as.numeric(as.character(x))
#' yA <- ifelse(x>=0.9,1,0)
#' yD <- ifelse(x<=-0.9,1,0)
#' out <- as.data.frame(cbind(yA,yD))
#' colnames(out) <- c("Amp","Del")
#' return(out)
#' }))
#' colnames(temp2) <- gsub("\\.cna","",colnames(temp2))
#' gen_dat <- as.data.frame(cbind(gen_dat[,-grep(".cna",colnames(gen_dat))],
#' temp2))
#' }
#'
#' # check that gen_dat is a binary matrix #
#' if(anyNA(apply(gen_dat, 2, function(x){anyNA(as.numeric(x[!is.na(x)]))}))){
#' warning("All genetic components were not numeric. Those which weren't will be removed")
#' gen_dat <- gen_dat[,-which(apply(gen_dat,2,function(x){anyNA(as.numeric(x[!is.na(x)]))}))]
#' }
#'
#' if(!all(apply(gen_dat,2,function(x){length(unique(x[!is.na(x)])) <= 2}))){
#' warning("All genetic components were not binary. Those which weren't will be removed")
#' gen_dat <- gen_dat[,-which(apply(gen_dat,2,function(x){length(unique(x[!is.na(x)])) > 2}))]
#' }
#'
#'
#' if(!is.null(clin_dat)){
#' # seet NA's to UNKNOWN #
#' clin_dat <- clin_dat %>%
#' tibble::rownames_to_column('sample') %>%
#' mutate_all(as.character) %>%
#' tibble::column_to_rownames('sample')
#' if(anyNA(clin_dat)) clin_dat[is.na(clin_dat)] <- "Unknown"
#' # subset data #
#' patients <- intersect(rownames(gen_dat),rownames(clin_dat))
#' gen_dat <- gen_dat[match(patients,rownames(gen_dat)),]
#' clin_dat <- clin_dat %>%
#' tibble::rownames_to_column('sample')
#' clin_dat <- clin_dat[match(patients,clin_dat$sample),]
#' rownames(clin_dat) <- clin_dat$sample
#' clin_dat <- clin_dat %>%
#' select(-one_of("sample"))
#' ## names ##
#' genes <- c(colnames(clin_dat),unique(gsub(".Amp|.Del|.fus","",colnames(gen_dat))))
#' }
#' else genes <- unique(gsub(".Amp|.Del|.fus","",colnames(gen_dat)))
#'
#' mat <- as.data.frame(matrix(nrow=length(genes),ncol=nrow(gen_dat)))
#' colnames(mat) <- rownames(gen_dat)
#' rownames(mat) <- genes
#'
#' # mutations #
#' mut <- gen_dat[,stats::na.omit(match(genes,colnames(gen_dat)))]
#'
#' for(i in 1:nrow(mut)){
#' for(j in 1:ncol(mut)){
#' if(!is.na(mut[i,j])){
#' if(mut[i,j]==1) {
#' mat[match(colnames(mut)[j],rownames(mat)),match(rownames(mut)[i],colnames(mat))] <- "MUT;"
#' }
#' }
#' else{
#' mat[match(colnames(mut)[j],rownames(mat)),match(rownames(mut)[i],colnames(mat))] <- "MIS;"
#' }
#' }
#' }
#'
#' # del #
#' if(length(stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))) > 0){
#' del <- gen_dat[,stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))]
#' if(is.null(dim(del))) {
#' del <- as.data.frame(del)
#' rownames(del) <- rownames(gen_dat)
#' }
#' colnames(del) <- gsub(".Del","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".Del"),colnames(gen_dat)))])
#' for(i in 1:nrow(del)){
#' for(j in 1:ncol(del)){
#' if(!is.na(del[i,j])){
#' if(del[i,j]==1) {
#' if(!is.na(mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))])){
#' mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))],"DEL;")}
#' else{mat[match(colnames(del)[j],rownames(mat)),match(rownames(del)[i],colnames(mat))] <- "DEL;"}
#' }
#' }
#' }
#' }
#' }
#'
#' # amp #
#' if(length(stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))) > 0){
#' amp <- gen_dat[,stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))]
#' if(is.null(dim(amp))) {
#' amp <- as.data.frame(amp)
#' rownames(amp) <- rownames(gen_dat)
#' }
#' colnames(amp) <- gsub(".Amp","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".Amp"),colnames(gen_dat)))])
#' for(i in 1:nrow(amp)){
#' for(j in 1:ncol(amp)){
#' if(!is.na(amp[i,j])){
#' if(amp[i,j]==1) {
#' if(!is.na(mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))])){
#' mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))],"AMP;")}
#' else{mat[match(colnames(amp)[j],rownames(mat)),match(rownames(amp)[i],colnames(mat))] <- "AMP;"}
#' }
#' }
#' }
#' }
#' }
#'
#' # fusions #
#' if(length(stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))) > 0){
#' fusion <- gen_dat[,stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))]
#' if(is.null(dim(fusion))) {
#' fusion <- as.data.frame(fusion)
#' rownames(fusion) <- rownames(gen_dat)
#' }
#' colnames(fusion) <- gsub(".fus","",colnames(gen_dat)[stats::na.omit(match(paste0(genes,".fus"),colnames(gen_dat)))])
#' for(i in 1:nrow(fusion)){
#' for(j in 1:ncol(fusion)){
#' if(!is.na(fusion[i,j])){
#' if(fusion[i,j]==1) {
#' if(!is.na(mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))])){
#' mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))] <-
#' paste0(mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))],"FUS;")}
#' else{mat[match(colnames(fusion)[j],rownames(mat)),match(rownames(fusion)[i],colnames(mat))] <- "FUS;"}
#' }
#' }
#' }
#' }
#' }
#' ### clin ###
#' if(!is.null(clin_dat)){
#' temp <- clin_dat
#' for(x in colnames(clin_dat)){
#' y <- clin_dat[,x]
#'
#' # if binary #
#' if(length(unique(y[!is.na(y)])) == 2){
#' mat[match(x,rownames(mat)),] <- paste0(x,"_",y,";") #ifelse(y==1,"CLIN;",NA)
#' }
#'
#' else if(length(unique(y[!is.na(y)])) %in% c(3:5)){
#' mat[match(x,rownames(mat)),] <- paste0(x,"_",y,";") #abbreviate(x,1)
#' }
#'
#' else{
#' y <- as.numeric(y)
#' mat[match(x,rownames(mat)),] <- ifelse(y > stats::median(y,na.rm = T),paste0(x,";"),NA)
#' }
#' }
#' }
#' ###
#' mat[is.na(mat)] <- " "
#' mat <- as.matrix(mat)
#'
#' return(mat)
#' }
#'
#'
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