Mercurial > repos > guerler > charts

changeset 14:61421ea8a3d4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author guerler
date Fri, 25 Apr 2014 20:05:22 -0400
parents e676c441d388
children 7dfaa61fecf7
files boxplot.r charts.r charts.xml histogram.r tool_dependencies.xml
diffstat 5 files changed, 0 insertions(+), 587 deletions(-) [+]
line wrap: on
line diff
--- a/boxplot.r	Fri Apr 18 21:41:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-wrapper <- function(table, columns, options) {
-
-    # initialize output list
-    l <- list()
-
-    # loop through all columns
-    for (key in names(columns)) {
-        # load column data
-        column <- as.numeric(columns[key])
-        column_data <- sapply( table[column], as.numeric )
-
-        # create hist data
-        data <- boxplot(column_data, plot=FALSE)
-        
-        # collect vectors in list
-        l <- append(l, list(data$stats))
-    }
-    
-    # return
-    return (l)
-}
--- a/charts.r	Fri Apr 18 21:41:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,459 +0,0 @@
-#!/usr/bin/Rscript
-
-#' Returns file name of calling Rscript
-#'
-#' \code{get_Rscript_filename} returns the file name of calling Rscript 
-#' @return A string with the filename of the calling script.
-#'      If not found (i.e. you are in a interactive session) returns NA.
-#'
-#' @export
-get_Rscript_filename <- function() {
-    prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
-    if( .Platform$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))] 
-}
-
-#' #!/path/to/Rscript
-#' library('getopt');
-#' #get options, using the spec as defined by the enclosed list.
-#' #we read the options from the default: commandArgs(TRUE).
-#' spec = matrix(c(
-#'   'verbose', 'v', 2, "integer",
-#'   'help'   , 'h', 0, "logical",
-#'   'count'  , 'c', 1, "integer",
-#'   'mean'   , 'm', 1, "double",
-#'   'sd'     , 's', 1, "double"
-#' ), byrow=TRUE, ncol=4);
-#' opt = getopt(spec);
-#' 
-#' # if help was asked for print a friendly message 
-#' # and exit with a non-zero error code
-#' if ( !is.null(opt$help) ) {
-#'   cat(getopt(spec, usage=TRUE));
-#'   q(status=1);
-#' }
-#' 
-#' #set some reasonable defaults for the options that are needed,
-#' #but were not specified.
-#' if ( is.null(opt$mean    ) ) { opt$mean    = 0     }
-#' if ( is.null(opt$sd      ) ) { opt$sd      = 1     }
-#' if ( is.null(opt$count   ) ) { opt$count   = 10    }
-#' if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
-#' 
-#' #print some progress messages to stderr, if requested.
-#' if ( opt$verbose ) { write("writing...",stderr()); }
-#' 
-#' #do some operation based on user input.
-#' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n"));
-#' cat("\n");
-#' 
-#' #signal success and exit.
-#' #q(status=0);
-getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {
-
-  # littler compatibility - map argv vector to opt
-  if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
-    opt = get("argv", envir = .GlobalEnv);
-  }
-
-  ncol=4;
-  maxcol=6;
-  col.long.name    = 1;
-  col.short.name   = 2;
-  col.has.argument = 3;
-  col.mode         = 4;
-  col.description  = 5;
-
-  flag.no.argument = 0;
-  flag.required.argument = 1;
-  flag.optional.argument = 2;
-
-  result = list();
-  result$ARGS = vector(mode="character");
-
-  #no spec.  fail.
-  if ( is.null(spec) ) {
-    stop('argument "spec" must be non-null.');
-
-  #spec is not a matrix.  attempt to coerce, if possible.  issue a warning.
-  } else if ( !is.matrix(spec) ) {
-    if ( length(spec)/4 == as.integer(length(spec)/4) ) {
-      warning('argument "spec" was coerced to a 4-column (row-major) matrix.  use a matrix to prevent the coercion');
-      spec = matrix( spec, ncol=ncol, byrow=TRUE );
-    } else {
-      stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
-    }
-
-  #spec is a matrix, but it has too few columns.
-  } else if ( dim(spec)[2] < ncol ) {
-    stop(paste('"spec" should have at least ",ncol," columns.',sep=''));
-
-  #spec is a matrix, but it has too many columns.
-  } else if ( dim(spec)[2] > maxcol ) {
-    stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));
-
-  #spec is a matrix, and it has some optional columns.
-  } else if ( dim(spec)[2] != ncol ) {
-    ncol = dim(spec)[2];
-  }
-
-  #sanity check.  make sure long names are unique, and short names are unique.
-  if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
-    stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
-  }
-  if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
-    stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
-  }
-  # convert numeric type to double type
-  spec[,4] <- gsub("numeric", "double", spec[,4])
-
-  # if usage=TRUE, don't process opt, but generate a usage string from the data in spec
-  if ( usage ) {
-    ret = '';
-    ret = paste(ret,"Usage: ",command,sep='');
-    for ( j in 1:(dim(spec))[1] ) {
-      ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep='');
-      if (spec[j,col.has.argument] == flag.no.argument) {
-        ret = paste(ret,']',sep='');
-      } else if (spec[j,col.has.argument] == flag.required.argument) {
-        ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
-      } else if (spec[j,col.has.argument] == flag.optional.argument) {
-        ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
-      }
-    }
-    # include usage strings
-    if ( ncol >= 5 ) {
-      max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
-      ret = paste(ret,"\n",sep='');
-      for (j in 1:(dim(spec))[1] ) {
-        ret = paste(ret,sprintf(paste("    -%s|--%-",max.long,"s    %s\n",sep=''),
-          spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description]
-        ),sep='');
-      }
-    }
-    else {
-      ret = paste(ret,"\n",sep='');
-    }
-    return(ret);
-  }
-
-  #XXX check spec validity here.  e.g. column three should be convertible to integer
-
-  i = 1;
-
-  while ( i <= length(opt) ) {
-    if ( debug ) print(paste("processing",opt[i]));
-
-    current.flag = 0; #XXX use NA
-    optstring = opt[i];
-
-
-    #long flag
-    if ( substr(optstring, 1, 2) == '--' ) {
-      if ( debug ) print(paste("  long option:",opt[i]));
-
-      optstring = substring(optstring,3);
-
-      this.flag = NA;
-      this.argument = NA;
-      kv = strsplit(optstring, '=')[[1]];
-      if ( !is.na(kv[2]) ) {
-        this.flag = kv[1];
-        this.argument = paste(kv[-1], collapse="=");
-      } else {
-        this.flag = optstring;
-      }
-
-      rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );
-
-      #long flag is invalid, matches no options
-      if ( length(rowmatch) == 0 ) {
-        stop(paste('long flag "', this.flag, '" is invalid', sep=''));
-
-      #long flag is ambiguous, matches too many options
-      } else if ( length(rowmatch) > 1 ) {
-        # check if there is an exact match and use that
-        rowmatch = which(this.flag == spec[,col.long.name])
-        if(length(rowmatch) == 0) {
-          stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
-        }
-      }
-
-      #if we have an argument
-      if ( !is.na(this.argument) ) {
-        #if we can't accept the argument, bail out
-        if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
-          stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
-
-        #otherwise assign the argument to the flag
-        } else {
-          storage.mode(this.argument) = spec[rowmatch, col.mode];
-          result[spec[rowmatch, col.long.name]] = this.argument;
-	  i = i + 1;
-	  next;
-        }
-
-      #otherwise, we don't have an argument
-      } else {
-        #if we require an argument, bail out
-        ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
-        ###  stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
-
-        #long flag has no attached argument. set flag as present.  set current.flag so we can peek ahead later and consume the argument if it's there
-        ###} else {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-          current.flag = rowmatch;
-        ###}
-      }
-
-    #short flag(s)
-    } else if ( substr(optstring, 1, 1) == '-' ) {
-      if ( debug ) print(paste("  short option:",opt[i]));
-
-      these.flags = strsplit(optstring,'')[[1]];
-
-      done = FALSE;
-      for ( j in 2:length(these.flags) ) {
-        this.flag = these.flags[j];
-        rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
-
-        #short flag is invalid, matches no options
-        if ( length(rowmatch) == 0 ) {
-          stop(paste('short flag "', this.flag, '" is invalid', sep=''));
-
-        #short flag is ambiguous, matches too many options
-        } else if ( length(rowmatch) > 1 ) {
-          stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
-
-        #short flag has an argument, but is not the last in a compound flag string
-        } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
-          stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
-
-        #short flag has no argument, flag it as present
-        } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-	  done = TRUE;
-
-        #can't definitively process this flag yet, need to see if next option is an argument or not
-        } else {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-          current.flag = rowmatch;
-          done = FALSE;
-        }
-      }
-      if ( done ) {
-        i = i + 1;
-        next;
-      }
-    }
-
-    #invalid opt
-    if ( current.flag == 0 ) {
-      stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
-      #TBD support for positional args
-      #if ( debug ) print(paste('"', optstring, '" not a valid option.  It is appended to getopt(...)$ARGS', sep=''));
-      #result$ARGS = append(result$ARGS, optstring);
-
-    # some dangling flag, handle it
-    } else if ( current.flag > 0 ) {
-      if ( debug ) print('    dangling flag');
-      if ( length(opt) > i ) {
-        peek.optstring = opt[i + 1];
-        if ( debug ) print(paste('      peeking ahead at: "',peek.optstring,'"',sep=''));
-
-        #got an argument.  attach it, increment the index, and move on to the next option.  we don't allow arguments beginning with '-' UNLESS
-	#specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
-        if ( substr(peek.optstring, 1, 1) != '-' |
-	  #match negative double
-	  ( substr(peek.optstring, 1, 1) == '-'
-	  & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
-	  & spec[current.flag, col.mode]== 'double'
-	  ) |
-	  #match negative integer
-	  ( substr(peek.optstring, 1, 1) == '-'
-	  & regexpr('^-[0123456789]+$',peek.optstring) > 0
-	  & spec[current.flag, col.mode]== 'integer'
-	  )
-	) {
-          if ( debug ) print(paste('        consuming argument *',peek.optstring,'*',sep=''));
-
-          storage.mode(peek.optstring) = spec[current.flag, col.mode];
-          result[spec[current.flag, col.long.name]] = peek.optstring;
-          i = i + 1;
-
-	#a lone dash
-	} else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
-          if ( debug ) print('        consuming "lone dash" argument');
-          storage.mode(peek.optstring) = spec[current.flag, col.mode];
-          result[spec[current.flag, col.long.name]] = peek.optstring;
-          i = i + 1;
-
-        #no argument
-        } else {
-          if ( debug ) print('        no argument!');
-
-          #if we require an argument, bail out
-          if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
-            stop(paste('flag "', this.flag, '" requires an argument', sep=''));
-
-          #otherwise set flag as present.
-          } else if (
-	    spec[current.flag, col.has.argument] == flag.optional.argument |
-	    spec[current.flag, col.has.argument] == flag.no.argument 
-	  ) {
-  	    x = TRUE;
-  	    storage.mode(x) = spec[current.flag, col.mode];
-            result[spec[current.flag, col.long.name]] = x;
-          } else {
-            stop(paste("This should never happen.",
-              "Is your spec argument correct?  Maybe you forgot to set",
-              "ncol=4, byrow=TRUE in your matrix call?"));
-	  }
-        }
-      #trailing flag without required argument
-      } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
-        stop(paste('flag "', this.flag, '" requires an argument', sep=''));
-
-      #trailing flag without optional argument
-      } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
-        x = TRUE;
-        storage.mode(x) = spec[current.flag, col.mode];
-        result[spec[current.flag, col.long.name]] = x;
-
-      #trailing flag without argument
-      } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
-        x = TRUE;
-        storage.mode(x) = spec[current.flag, col.mode];
-        result[spec[current.flag, col.long.name]] = x;
-      } else {
-        stop("this should never happen (2).  please inform the author.");
-      }
-    #no dangling flag, nothing to do.
-    } else {
-    }
-
-    i = i+1;
-  }
-  return(result);
-}
-
-# convert multi parameter string (i.e. key1: value, key2: value, ...) to object
-split <- function(argument){
-    # process parameter string
-    options <- list()
-    list <- gsub("\\s","", argument)
-    list <- strsplit(list, ",")
-    if (length(list) > 0) {
-        list <- list[[1]]
-        for (entry in list) {
-            pair <- strsplit(entry, ":")
-            if (length(pair) > 0) {
-                pair <- pair[[1]]
-                if (length(pair) == 2) {
-                    options[[pair[1]]] <- pair[2]
-                }
-            }
-        }
-    }
-    return(options)
-}
-
-# get options, using the spec as defined by the enclosed list.
-spec = matrix(c(
-    'workdir',  'w', 1, 'character', 'Work directory',
-    'module',   'm', 1, 'character', 'Module name',
-    'input',    'i', 1, 'character', 'Input tabular file',
-    'columns',  'c', 1, 'character', 'Columns string',
-    'settings', 's', 1, 'character', 'Settings string',
-    'output',   'o', 1, 'character', 'Output tabular file',
-    'help',     'h', 0, '',          'Help',
-    'verbose',  'v', 0, '',          'Verbose'
-), byrow=TRUE, ncol=5);
-opt = getopt(spec);
-
-# show help
-if ( !is.null(opt$help) ||
-    is.null(opt$module) ||
-    is.null(opt$input) ||
-    is.null(opt$columns) ||
-    is.null(opt$output)) {
-    cat(getopt(spec, usage=TRUE))
-    q(status=1);
-}
-
-# read columns/settings
-columns = split(opt$columns)
-settings = split(opt$settings)
-
-# read table
-table <- read.table(opt$input)
-
-# identify module file
-module_file = paste(opt$workdir, opt$module, '.r', sep='')
-
-# source module
-source(module_file)
-
-# run module
-l = wrapper (table, columns, settings)
-
-# header
-header_title <- '# title - Chart Utilities (charts)'
-header_date <- paste('# date -', Sys.time(), sep=' ')
-header_module <- paste('# module -', opt$module, sep=' ')
-header_settings <- paste('# settings -', opt$settings, sep=' ')
-header_columns <- paste('# columns -', opt$columns, sep=' ')
-
-# fill gaps
-if (length(l) > 0) {
-    # print details
-    if (!is.null(opt$verbose)) {
-        print ('Columns:')
-        print (columns)
-        print ('Settings:')
-        print (settings)
-        print ('Result:')
-        print (l)
-    }
-
-    # create output file
-    output <- file(opt$output, open='wt')
-    
-    # write header
-    writeLines('#', output)
-    writeLines(header_title, output)
-    writeLines(header_date, output)
-    writeLines(header_module, output)
-    writeLines(header_settings, output)
-    writeLines(header_columns, output)
-    writeLines('#', output)
-    
-    # write table
-    write.table(l, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
-    
-    # close file
-    close(output)
-} else {
-    print ('Columns:')
-    print (columns)
-    print ('Settings:')
-    print (settings)
-    print ('No output generated.')
-}
\ No newline at end of file
--- a/charts.xml	Fri Apr 18 21:41:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="charts" name="Charts" version="1.0.0">
-    <hidden>True</hidden>
-    <description>wrapper for R</description>
-    <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="2.15.0">R</requirement>
-    </requirements>
-    <command>Rscript \$SCRIPT_PATH/charts.r -w \$SCRIPT_PATH/ -m ${module} -i ${input} -c '${columns}' -s '${settings}' -o ${output}
-    </command>
-    <inputs>
-        <param name="input" type="data" label="Input dataset" format="tabular" />
-        <param name="module" type="select" label="R-script">
-            <option value="histogram">Histogram</option>
-            <option value="boxplot">Box plot</option>
-        </param>
-        <param name="columns" type="text" label="Columns string (i.e key1: column, key2: column)" value="column: 2"/>
-        <param name="settings" type="text" label="Options string (i.e data_limit: 1000)" value=""/>
-    </inputs>
-    <outputs>
-        <data name="output" format="tabular" />
-    </outputs>
-</tool>
\ No newline at end of file
--- a/histogram.r	Fri Apr 18 21:41:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-# utilities
-boundary <- function(x, increment) {
-    return (floor(x / increment) * increment)
-}
-
-roundup <- function(x) {
-    return (sign(x) * 10^ceiling(log10(abs(x))))
-}
-
-# wrapper
-wrapper <- function(table, columns, options) {
-
-    # initialize output list
-    l <- list()
-
-    # loop through all columns
-    m <- list()
-    for (key in names(columns)) {
-        # load column data
-        column <- as.numeric(columns[key])
-        column_data <- sapply( table[column], as.numeric )
-
-        # collect vectors in list
-        m <- append(m, list(column_data))
-    }
-    
-    # get min/max boundaries
-    min_value <- min(unlist(m))
-    max_value <- max(unlist(m))
-    
-    # identify increment
-    increment <- roundup((max_value - min_value) / 10)
-    
-    # fix min value
-    min_value <- boundary(min_value, increment)
-    
-    # fix max value
-    max_value <- min_value + increment * 10
-    
-    # check if single bin is enough
-    if (min_value == max_value) {
-        l <- append(l, max_value)
-        for (key in seq(m)) {
-            l <- append(l, 1.0)
-        }
-        return (l)
-    }
-    
-    # fix range and bins
-    bin_seq = seq(min_value, max_value, by=increment)
-    
-    # add as first column
-    l <- append(l, list(bin_seq[2: length(bin_seq)]))
-    
-    # loop through all columns
-    for (key in seq(m)) {
-        # load column data
-        column_data <- m[[key]]
-        
-        # create hist data
-        hist_data <- hist(column_data, breaks=bin_seq, plot=FALSE)
-        
-        # normalize densities
-        count_sum <- sum(hist_data$counts)
-        if (count_sum > 0) {
-            hist_data$counts = hist_data$counts / count_sum
-        }
-
-        # collect vectors in list
-        l <- append(l, list(hist_data$counts))
-    }
-    
-
-    # return
-    return (l)
-}
--- a/tool_dependencies.xml	Fri Apr 18 21:41:34 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="R" version="2.15.0">
-        <repository changeset_revision="6a72f1ba7293" name="package_r_2_15_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>