annotate src/utils.R @ 0:708f43bda2b6 draft

"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"

# Copyright (c) 2011-2013 Trevor L. Davis <[e-mail]>  
#  
#  This file is free software: you may copy, redistribute and/or modify it  
#  under the terms of the GNU General Public License as published by the  
#  Free Software Foundation, either version 2 of the License, or (at your  
#  option) any later version.  
#  
#  This file is distributed in the hope that it will be useful, but  
#  WITHOUT ANY WARRANTY; without even the implied warranty of  
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  
#  General Public License for more details.  
#  
#  You should have received a copy of the GNU General Public License  
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.  


#extendedDist function to correlation measure
distExtended <- function(x,method) {
  if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"))return(dist(x,method = method))
  if(method %in% c("pearson", "spearman", "kendall"))return(as.dist(1-cor(t(x),method=method))/2)
  if(method %in% c("absPearson", "absSpearman", "absKendall"))return(as.dist(1-abs(cor(t(x),method=method))))
  return(NULL)
}

##comment function to display message and optionnaly add it to log file

addComment <- function(text,addToFile=FALSE,fileName=NULL,append=TRUE,display=TRUE){
  if(display)cat(paste(c(text,"\n"),collapse = " ")) 
  if(addToFile)write(paste(text,collapse = " "),fileName,append=append)
}

printSessionInfo <- function(fileName=NULL,append=TRUE){
  addComment("[INFO]R session info :",T,fileName,display=FALSE)
  tempInfo=sessionInfo()
  write(paste(tempInfo$R.version$version.string),fileName,append=append)
  write(paste("Platform",tempInfo$platform,sep = " : "),fileName,append=append)
  write(paste("Running under",tempInfo$running,sep = " : "),fileName,append=append)
  write(paste("Local variables",tempInfo$locale,sep = " : "),fileName,append=append)
  write(paste("Attached base packages",paste(tempInfo$basePkgs,collapse = "; "),sep = " : "),fileName,append=append)
  if(length(tempInfo$otherPkgs)>0){
    lineToPrint=""
    for(iPack in tempInfo$otherPkgs){
      lineToPrint=paste(lineToPrint,iPack$Package," ",iPack$Version,"; ",sep = "")
    }
    write(paste("Other attached packages",lineToPrint,sep = " : "),fileName,append=append)
  }
  if(length(tempInfo$loadedOnly)>0){
    lineToPrint=""
    for(iPack in tempInfo$loadedOnly){
      lineToPrint=paste(lineToPrint,iPack$Package," ",iPack$Version,"; ",sep = "")
    }
    write(paste("Loaded packages",lineToPrint,sep = " : "),fileName,append=append)
  }
}

##negative of a mathematical expression
negativeExpression <- function(expression){
  expression=gsub("\\+","_toMinus_",expression)
  expression=gsub("\\-","+",expression)
  expression=gsub("_toMinus_","-",expression)
  if(substr(expression,1,1)!="-" && substr(expression,1,1)!="+"){
    expression=paste(c("-",expression),collapse="")
  }

  return(expression)
}

#' Returns file name of calling Rscript
#'
#' \code{get_Rscript_filename} returns the file name of calling Rscript 
#' @return A string with the filename of the calling script.
#'      If not found (i.e. you are in a interactive session) returns NA.
#'
#' @export
get_Rscript_filename <- function() {
    prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
    if( .Platform$OS.type == "windows") { 
        prog <- gsub("\\\\", "\\\\\\\\", prog)
    }
    prog
}

#' Recursively sorts a list
#'
#' \code{sort_list} returns a sorted list
#' @param unsorted_list A list.
#' @return A sorted list.
#' @export
sort_list <- function(unsorted_list) {
    for(ii in seq(along=unsorted_list)) {
        if(is.list(unsorted_list[[ii]])) {
            unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]])
        }
    }
    unsorted_list[sort(names(unsorted_list))] 
}


# Multiple plot function
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols:   Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
#
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
#
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
  library(grid)
  
  # Make a list from the ... arguments and plotlist
  plots <- c(list(...), plotlist)
  
  numPlots = length(plots)
  
  # If layout is NULL, then use 'cols' to determine layout
  if (is.null(layout)) {
    # Make the panel
    # ncol: Number of columns of plots
    # nrow: Number of rows needed, calculated from # of cols
    layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
                     ncol = cols, nrow = ceiling(numPlots/cols))
  }
  
  if (numPlots==1) {
    print(plots[[1]])
    
  } else {
    # Set up the page
    grid.newpage()
    pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
    
    # Make each plot, in the correct location
    for (i in 1:numPlots) {
      # Get the i,j matrix positions of the regions that contain this subplot
      matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
      
      print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
                                      layout.pos.col = matchidx$col))
    }
  }
}