Package 'HilbertVisGUI'

Title: HilbertVisGUI
Description: An interactive tool to visualize long vectors of integer data by means of Hilbert curves
Authors: Simon Anders <[email protected]>
Maintainer: Simon Anders <[email protected]>
License: GPL (>= 3)
Version: 1.71.1
Built: 2026-05-29 21:56:50 UTC
Source: https://github.com/bioc/HilbertVisGUI

Help Index

List apply for '...' arguments

Description

A kludge to get around a certain problem in using lapply with '...' ellipsis function arguments.

Usage

dotsapply( fun, ... )

Arguments

fun

A function that takes one argument
...

Arguments to which the function should be applied

Details

"dotsapply(fun,...)" gives the same result as lapply( list(...), fun). However, the construction with "list", when used for variables enumerated explicitely, will result in their duplication.

Assume, for example, that you have three very large vectors a, b, and c, whose lengths you wish to know. If your write "lapply( list(a,b,c), length )", R will duplicate all three vectors in memory when constructing the list, which results in unnecessary use of memory. The alternative "dotsapply( length, a, b, c )" avoids this. Of course, you could also write "list( length(a), length(b), length(c) )", which neither causes duplication.

This last possibility is, however, not an option, if, instead of "a,b,c", you have ellipsed function arguments, i.e. literally "...". In this special case, dotsapply comes in handy, and as this case arose in hilbertDisplay, I implemented dotsapply as a kludge and export it from the package just in case somebody ahs use for it.

Value

A list of function values

Author(s)

Simon Anders, EMBL-EBI, [email protected]

Hilbert curve visualization

Description

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

See the vignette for a full explanation.

Usage

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 )

Arguments

...

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.

palettePos

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.
paletteNeg

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

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.
naColor

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.
plotFunc

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.
names

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

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.
pow2

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.
portrait

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.
fullLengths

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.

Value

Returns an invisible NULL.

Author(s)

Simon Anders, EMBL-EBI, [email protected]

See Also

simpleLinPlot

Examples

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

Show up to three data vectors in the Hilbert curve display GUI.

Description

This is a variant of hilbertDisplay that takes up to three long data vector but does not display them in different panels (allowing to switch with the “Previous” and “Next” buttons but instead put them in one picture, using the three colour channels to overlay them. This is look for correlations in spatial distribution of the different data vectors.

Usage

hilbertDisplayThreeChannel(
   dataRed, 
   dataGreen = 0, 
   dataBlue = 0, 
   naColor = col2rgb("gray"), 
   fullLength = max(length(dataRed), length(dataGreen), length(dataBlue)), 
   portrait = FALSE)

Arguments

dataRed

The data to be displayed in the red colour channel, to be provided as a numeric vector with values between 0 (black) and 1 (bright red). You may either pass an ordinary R vector or an Rle vector as defined in the IRanges package.
dataGreen

As dataRed but for the green channel.

dataBlue

As dataRed but for the blue channel.

naColor

The color to use to indicate NA.

fullLength

The vector length that should correspond to the full display. By default, the length of the longest data vector. It may make sense to round up to the next power of two.

portrait

Whether to arrange the buttons to the right of the display. Useful on small screens.

Value

Invisible NULL.

Note

This function is a bit less mature than the function hilbertDisplay. Especially, the GUI functions “Linear plot”, “Previous”, and “Next” are displayed but defunct.

Author(s)

Simon Anders

See Also

hilbertDisplay

Default plot callback function for hilbertDisplay

Description

Plots a small part of the supplied vector.

Usage

simpleLinPlot( data, info )

Arguments

data

The data vector, a vector of integers.
info

A list with fields describing the context, as described in the help page for hilbertDisplay.

Details

This is a very simple function that is called by default by hilbertDisplay when the user chooses the "Linear plot" option and clicks on a pixel in the display. It displays a piece of 2000 values of the data vector, centered around info$bin. You will often want to replace this function by one tailored to your needs.

Value

Null.

Author(s)

Simon Anders, EMBL-EBI, [email protected]

See Also

hilbertDisplay