runGMT: Run GMT
In sherrillmix/GMTHexMapR: Generate a hexmap from position data

Takes files generated by previous functions and calls mapping program GMT to generate output postscript file IMPORTANT: You must have GMT installed for this function to work

runGMT(limits, outFile = "output.ps", width = 6, dataFile = "hexs.dat",
  gmtDir = "", scale = TRUE, contourFile = NULL, contourDepth = -200,
  extraCmd = NULL, landMaskCmd = NULL, landMask = TRUE, ps2eps = FALSE,
  scaleLabel = "Days Turtles Recorded in Hex", contourPen = "1/120ta",
  concatenate = FALSE, xpos = 3, ypos = 1.8,
  posOptions = ifelse(concatenate, "-O", ""), gmtsetOptions = NULL,
  annotateBorders = "WSen", borderColor = 255, pscoastOptions = "")

`limits`	Vector of (lowXLim,highXlim,lowYLim,highYLim) probably from makeHexs or passed in from hexPlot
`outFile`	File location to output GMT postscript to
`width`	Width of output figure in inches
`dataFile`	File location of hex color and lat/lon data previously generated by makeHexs
`gmtDir`	System directory for calling GMT functions (e.g. if pscoast is in /home/bin/ and /home/bin/ isn't in path then gmtDir="/home/bin/")
`scale`	If TRUE make a scale based on files output by makeTicks (called in makeHexs)
`contourFile`	If not NULL, run pscontour at contourDepth meters based on this GMT elevation file
`contourDepth`	Depth to draw contour in meters
`extraCmd`	If not NULL, vector of system commands to run after other GMT commands and before scale (e.g. extra labels with pstext)
`landMaskCmd`	If not NULL, vector of system commands to run prior to final psCoast (e.g. polygons overlaid by coast)
`landMask`	If TRUE, hexs overlapping land are covered by land else hexs overlap land and only the land border is plotted over them
`ps2eps`	If TRUE, after all other commands calls the program ps2eps to convert .ps to .eps (Make sure you have ps2eps installed and in path if you use this)
`scaleLabel`	Label for scale if scale is TRUE
`contourPen`	A string or vector of strings specifying pen attributes for grd contour to trace the contour file
`concatenate`	Add output to existing file?
`xpos`	Shift plot origin right xpos inches
`ypos`	Shift plot origin up ypos inches
`posOptions`	Options for position (e.g. -O)
`gmtsetOptions`	Options for gmtset
`annotateBorders`	A string like "WSen" specifying which borders to annotate as in psbasemap
`borderColor`	color for border of hexes
`pscoastOptions`	command line options for pscoast