See the vignette for a full explanation.
hilbertDisplay( ..., palettePos = colorRampPalette( c( "white", "red" ) )( 300 ), paletteNeg = colorRampPalette( c( "white", "blue" ) )( length(palettePos) ), maxPaletteValue = NULL, naColor = "gray", plotFunc = simpleLinPlot, names=NULL, sameScale=TRUE, pow2=FALSE, portrait=TRUE, fullLengths = NULL )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. 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.substitute
are used.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.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.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.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.simpleLinPlot
random <- c( as.integer( runif(100000)*30 ) )
ramp <- c( as.integer( 0:19999/100 ) )
try( hilbertDisplay( random, ramp ) )
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