#' @title Function to produce an interactive heatmap using plot.ly
#' @description This function generates an heatmap using a count table and a specific gene list
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param scratch.folder, a character string indicating the scratch folder where docker container will be mounted
#' @param count.table, a character string indicating the path of the counts table file
#' @param gene.list, a character string indicating the path of the file containing the genes to include in the heatmap
#' @param output.folder, a character string indicating the path of the output folder
#' @param separator, a character string indicating the separator character in the count table. Allowed characters are TAB, COMMA and SPACE
#' @param status, a character string, 'raw' if the data are raw counts, 'log' otherwise
#' @param color.palette, a string indicating the color palette to be used in the heatmap. Available palettes are Viridis, BrBG, magma, plasma and cividis
#' @author Nicola Licheri, nicola [dot] licheri [at] unito [dot] it, University of Turin
#'
#' @return A html file containing the interactive heatmap produced using plot.ly
#' @examples
#'\dontrun{
#'
#' }
#' @export
heatmaply <- function(group=c("docker", "sudo"), scratch.folder, count.table, gene.list, output.folder,
separator=c("TAB", "COMMA", "SPACE"), status=c("raw", "log"),
color.palette=c("viridis", "BrBG", "magma", "plasma", "cividis")) {
#running time 1
ptm <- proc.time()
#obtaining absolute paths
count.table <- normalizePath(count.table)
gene.list <- normalizePath(gene.list)
scratch.folder <- normalizePath(scratch.folder)
output.folder <- normalizePath(output.folder)
data.folder <- output.folder
#storing the position of the home folder
home <- getwd()
setwd(data.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#check if scratch folder exist
if (!file.exists(scratch.folder)){
cat(paste("\nIt seems that", scratch.folder, "folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(data.folder)
return(3)
}
#check if output folder exist
if (!file.exists(output.folder)) {
cat(paste("\nIt seems that", output.folder, "folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(data.folder)
return(3)
}
#check if input data actually exist
if (!file.exists(count.table)) {
cat(paste("\nIt seems that", count.table, "file does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(data.folder)
return(3)
}
if (!file.exists(gene.list)) {
cat(paste("\nIt seems that", gene.list, "file does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(data.folder)
return(3)
}
params <- paste(
"--cidfile", paste0(data.folder, "/dockerID"),
"-v", paste0(count.table, ":/data/in/count_table"),
"-v", paste0(gene.list, ":/data/in/gene_list"),
"-v", paste0(output.folder, ":/data/out"),
"-v", paste0(scratch.folder, ":/scratch"),
"-d", "docker.io/repbioinfo/heatmap.2019.01",
"/bin/bash /bin/heatmap.sh", color.palette, separator, status
)
resultRun <- runDocker(group=group, params=params)
if (resultRun == 0) {
cat("Heatmaply terminated successfully.\n")
} else {
cat("Heatmaply terminated with errors.\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(data.folder)
dir <- dir[grep("run.info",dir)]
if(length(dir)>0) {
con <- file("run.info", "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
} else {
tmp.run <- NULL
tmp.run[1] <- paste("run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
#saving log and removing docker container
container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
system(paste0("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/", "heatmaply_", substr(container.id,1,12),".log"))
system(paste("docker rm", container.id))
# removing temporary files
cat("\n\nRemoving the temporary file ....\n")
system("rm -fR out.info")
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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