title: Vector from with read.table R
body: <p>I think I might be overcomplicating this in my mind. I have a file that I want to use to make a barplot in R. The file looks like this:</p>
  
  <pre><code>## metadata
  # filepath
  ## filename
  # Started on: Tue Jul 30 10:46:57 EDT 2013
  
  
  #HISTOGRAM    java.lang.Integer
  READ:  1    2
  -1  28  28
   0  27  29
  </code></pre>
  
  <p>I want to make a bar graph of the data I have. I was thinking it would look somewhat like this:</p>
  
  <pre><code>  |
    |
  # |             |   
    |  |          |
    |  |     |    |
    |__|_____|____|___|____
    -1(1) -1(2) 0(1) 0(2)
  </code></pre>
  
  <p>But I am having trouble reading in the data correctly. This is my code: </p>
  
  <pre><code># Parse the arguments
  args &lt;- commandArgs(trailing=T)
  #Chart file
  metricsFile  &lt;- args[1]
  #pdf file path and name that I want to produce
  outputFile   &lt;- args[2]
  
  # Figure out where the firstLine and the chart are in the file and parse them out
  startFinder &lt;- scan(metricsFile, what="character", sep="\n", quiet=TRUE, blank.lines.skip=FALSE)
  firstBlankLine=0
  #finds empty strings
  for (i in 1:length(startFinder))
  {
          if (startFinder[i] == "") {
                  if (firstBlankLine==0) {
                          firstBlankLine=i+1
                  } else {
                          secondBlankLine=i+1
                          break
                  }
          }
  }
  
   #I accept some args and I read past some header information 
  firstLine &lt;- read.table(metricsFile, header=T, nrows=1, sep="\t", skip=firstBlankLine)
  #prints "firstLine:  -1" "firstLine:  28" "firstLine:  28" 
  secondLine &lt;- read.table(metricsFile, header=T, nrows=1, sep="\t", skip=secondBlankLine)
  #prints "secondLine:  -1" "secondLine:  27" "secondLine:  29"
  
  # Then plot as a PDF
  pdf(outputFile)
  #I am just inputing firstLine here because I was trying to see how it works
  #I get the error:'height' must be a vector or a matrix
  barplot(firstLine,
          main=paste("Read",(i-1)," Distribution ",
          xlab="Counts",
          ylab="F/R Orientation")
  
  dev.off()
  </code></pre>
  
  <p>As I commented in my  code I get the error that 'height' must be a vector or matrix. I don't know R well enough to know how to read it in as a vector rather than how I am currently doing it. I also am not sure if perhaps the problem is that I am using barplot. Could it be that just 'plot' is better to use? Perhaps I am using read.table incorrectly? </p>