hilbertDisplay: Hilbert curve visualization

Description Usage Arguments Value Author(s) See Also Examples

View source: R/HilbertCurveDisplay.R


Display one or several long integer vectors in an interactive fashion by means of the Hilbert curve.

See the vignette for a full explanation.


      palettePos = colorRampPalette( c( "white", "red" ) )( 300 ),
      paletteNeg = colorRampPalette( c( "white", "blue" ) )( length(palettePos) ),
      maxPaletteValue = NULL,
      naColor = "gray", 
      plotFunc = simpleLinPlot, 
      fullLengths = NULL )



The data vectors to be visualized. This may be integer or real vectors, either as ordinary R vectors or as Rle vectors (as defined in the IRanges packages). Care is taken within hilbertDisplay that these vectors do not get duplicated, so that you can pass very large vectors.


The color palette used to visualize positive valued bins in the data. This must be either be a character vector of valid color names. If no palette is supplied, a ramp from white to red is used.


The color palette for bins with negative values. Both palettes must have the same number of colours.


The absolute bin value that should correspond to the end of the two palettes. (The beginning of the palettes always represents 0.) Within the graphical user interface, buttons are provided to adjust this interactively. If no value is provided, the median of the absolute values of maxima and minima of the data vectors is used.


The color to be used for bins which contain NAs or correspond to data outside the limits of the data vector. Pass a color name or a triple of RGB values. By default, "gray" is used.


An R function that is called if you use the "Linear plot" function offer by HilbertCurveDisplay's GUI. If you enable this function and then click on a pixel in the display, the function supplied as plotFunc is called. If you do not supply this parameter, the function simpleLinPlot (part of this package) is used. If you supply your own function, it must accept two parameters: data and info. data will be the currently displayed data vector. Be careful that your function does not duplicate it (check with tracemem, if in doubt) in order to avoid performance problems when dealing with large data. The second argument, info, is a list, supplying the following fields, all of which, except for the last one, are single integers: info$binLo, info$bin, and info$binHi are the lower, middle, and upper coordinate (i.e., vector index) of the bin represented by the pixel onto which the user has clicked. info$dispLo and info$dispHi are the lowest and highest index of the part of the vector currently displayed. info$seqIdx is the index of the currently displayed vector (i.e., its position in the '...' argument) and ionfo$seqName is its name. All indices are one-based. Your function should plot a region of interest around data[info$bin], or do some other useful operation. Any return value is ignored. For a very simple example, see the body of simpleLinPlot.


The names of the sequences. A character vector. If not supplied, the expressions used in the '...' argument, as reported by substitute are used.


Setting this argument to TRUE pads all but the largest vector with NAs such that all vectors have the same length. (The padding is done "virtually", i.e. no dupliocation in memory occurs.) The purpose of this is to make sure that the bin size (i.e. the number of values depicted by one pixel) stays constant, when using the DisplayHilbertViewer GUI's "Prev" and "Next" buttons, which switch the display through the supplied data vectors.


Setting thsi argument to TRUE pads all vectors virtually with NAs such that their length becomes a power of 2. The purpose of this becomes apparent if you zoom in so much that several pixels correspond to the same data vector element. Then, without this options, the values take on strange fractal forms, while they are square in case of a power-of-2 length.


Setting this option to FALSE changes the GUI layout such that the controls appear to the right of the curve display ("landscape layout") as opposed to the usual case of them appearing below ("portrait layout"). This is useful for small screens as the GUI window may be two tall to fit on the screen in portrait mode.


This option allows you to manually control the padding of vectors with NAs if you do not like the result of the same.scale or pow2 option. Supply an integer vector with as many values as their are vectors in the '...' argument, specifying the length including padding for each data vector. Passing numbers smaller than the length of the data.vector results in only the beginning of the vector being displayed.


Returns an invisible NULL.


Simon Anders, EMBL-EBI, sanders@fs.tum.de

See Also



random <- c( as.integer( runif(100000)*30 ) ) 
ramp <- c( as.integer( 0:19999/100 ) )
try( hilbertDisplay( random, ramp ) )

Example output

Loading required package: HilbertVis
Loading required package: grid
Loading required package: lattice

 | Cannot connect to an X display. Most functionality of 
 | HilbertVisGUI will be unavailable. Make sure that the DISPLAY
 | environment variable is set properly.

Warning message:
In dyn.load(file, DLLpath = DLLpath, ...) : Cannot connect to X display.
Error in hilbertDisplay(random, ramp) : 
  R_display_hilbert: X display unavailable.

HilbertVisGUI documentation built on Nov. 8, 2020, 5:48 p.m.