xVisInterpAnimate | R Documentation

## Function to animate the visualisation of interpolated irregular data

### Description

`xVisInterpAnimate` is supposed to animate the visualisation of interpolated irregular data. The output can be a pdf file containing a list of frames/images, a mp4 video file or a gif file. To support video output file, the software 'ffmpeg' must be first installed (also put its path into the system PATH variable; see Note). To support gif output file, the software 'ImageMagick' must be first installed (also put its path into the system PATH variable; see Note).

### Usage

    xVisInterpAnimate(ls_xyz, interpolation = c("spline", "linear"), nx =
    100,
    ny = 100, zlim = NULL, colkey = TRUE, contour = FALSE,
    image = FALSE, clab = c("Value"), nlevels = 20, colormap = "terrain",
    label.pch = 17, label.text.cex = 0.8, label.text.adj = -0.4,
    label.text.adj.z = 0.01, label.font.family = "sans", xy.swap = FALSE,
    theta.3D = 0, phi.3D = 20, verbose = TRUE,
    filename = "xVisInterpAnimate", filetype = c("pdf", "mp4", "gif"),
    image.type = c("jpg", "png"), image.bg = "transparent",
    height.device = NULL, num.frame = 36, sec_per_frame = 1, res = 72)

### Arguments

`ls_xyz` | a list with 3 required components (x, y and z) and an optional component (label)
`interpolation` | the method for the interpolation. It can be "linear" or "spline" interpolation
`nx` | the dimension of output grid in x direction
`ny` | the dimension of output grid in y direction
`zlim` | the minimum and maximum z values, defaulting to the range of the finite values of z

`colkey`

a logical (TRUE by default) or a 'list' with parameters for the color key (legend). List parameters should be one of 'side, plot, length, width, dist, shift, addlines, col.clab, cex.clab, side.clab, line.clab, adj.clab, font.clab'. The defaults for the parameters are 'side=4, plot=TRUE, length=1, width=1, dist=0, shift=0, addlines=FALSE, col.clab=NULL, cex.clab=par("cex.lab"), side.clab=NULL, line.clab=NULL, adj.clab=NULL, font.clab=NULL'. colkey=list(side=4,length=0.15,width=0.5,shift=0.35,dist=-0.15,cex.axis=0.6,cex.clab=0.8,side.clab=3)

`contour` | a logical (FALSE by default) or a 'list' with parameters for the contour function. An optional parameter to this 'list' is the 'side' where the image should be plotted. Allowed values for 'side' are a z-value, or 'side = "zmin", "zmax"', for positioning at bottom or top respectively. The default is to put the image at the bottom
`image` | a logical (FALSE by default) or a 'list' with parameters for the image2D function. An optional parameter to this 'list' is the 'side' where the image should be plotted. Allowed values for 'side' are a z-value, or 'side = "zmin", "zmax"', for positioning at bottom or top respectively. The default is to put the image at the bottom
`clab` | a title for the colorbar. the label to be written on top of the color key; to lower it, 'clab' can be made a vector, with the first values empty strings.
`nlevels` | the number of levels to partition the input matrix values. The same level has the same color mapped to

`colormap`

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

`label.pch` | a numeric value specifying the graphiics symbol (by default, 17 for upward triangle). This argument only works when the labelling is enabled
`label.text.cex` | a numeric value specifying the text size. This argument only works when the labelling is enabled
`label.text.adj` | a numeric value adjusting the text location in xy-plane. This argument only works when the labelling is enabled
`label.text.adj.z` | a numeric value adjusting the text locaion in z-axis. This argument only works when the labelling is enabled
`label.font.family` | the font family for texts. This argument only works when the labelling is enabled
`xy.swap` | logical to indicate whether to wrap x and y. By default, it sets to false
`theta.3D` | the starting azimuthal direction. By default, it is 0
`phi.3D` | the colatitude direction. By default, it is 20
`verbose` | logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
`filename` | the without-extension part of the name of the output file. By default, it is 'xVisInterpAnimate'
`filetype` | the type of the output file, i.e. the extension of the output file name. It can be one of either 'pdf' for the pdf file, 'mp4' for the mp4 video file, 'gif' for the gif file
`image.type` | the type of the image files temporarily generated. It can be one of either 'jpg' or 'png'. These temporary image files are used for producing mp4/gif output file. The reason doing so is to accommodate that sometimes only one of image types is supported so that you can choose the right one
`image.bg` | the background color for each frame/image. This argument only works when producing mp4 video or gif file
`height.device` | a numeric value specifying the height (or width) of device/frame/image.
`num.frame` | a numeric value specifying the number of frames/images. By default, it sets to the number of columns in the input data matrix
`sec_per_frame` | a numeric value specifying how long (seconds) it takes to stream a frame/image. This argument only works when producing mp4 video or gif file
`res` | the resolution for each frame/image. This argument only works when producing mp4 video or gif file

### Value

If specifying the output file name (see argument 'filename' above), the output file is either 'filename.pdf' or 'filename.mp4' or 'filename.gif' in the current working directory. If no output file name specified, by default the output file is either 'xVisInterpAnimate.pdf' or 'xVisInterpAnimate.mp4' or 'xVisInterpAnimate.gif'

### Note

When producing mp4 video, this function requires the installation of the software 'ffmpeg' at https://www.ffmpeg.org. Shell command lines for ffmpeg installation in Terminal (for both Linux and Mac) are:

- 1) `wget -O ffmpeg.tar.gz http://www.ffmpeg.org/releases/ffmpeg-2.7.1.tar.gz`

- 2) `mkdir ~/ffmpeg | tar xvfz ffmpeg.tar.gz -C ~/ffmpeg --strip-components=1`

- 3) `cd ffmpeg`

- 4a) # Assuming you want installation with a ROOT (sudo) privilege:
  `./configure --disable-yasm`

- 4b) # Assuming you want local installation without ROOT (sudo) privilege:
  `./configure --disable-yasm --prefix=$HOME/ffmpeg`

- 5) `make`

- 6) `make install`

- 7) # add the system PATH variable to your ~/.bash_profile file if you follow 4b) route:
  `export PATH=$HOME/ffmpeg:$PATH`

- 8) # make sure ffmpeg has been installed successfully:
  `ffmpeg -h`

When producing gif file, this function requires the installation of the software 'ImageMagick' at http://www.imagemagick.org. Shell command lines for ImageMagick installation in Terminal are:

- 1) `wget http://www.imagemagick.org/download/ImageMagick.tar.gz`

- 2) `mkdir ~/ImageMagick | tar xvzf ImageMagick.tar.gz -C ~/ImageMagick --strip-components=1`

- 3) `cd ImageMagick`

- 4) `./configure --prefix=$HOME/ImageMagick`

- 5) `make`

- 6) `make install`

- 7) # add the system PATH variable to your ~/.bash_profile file.
  For Linux:
  `export MAGICK_HOME=$HOME/ImageMagick`
  `export PATH=$MAGICK_HOME/bin:$PATH`
  `export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+$LD_LIBRARY_PATH:}$MAGICK_HOME/lib`
  For Mac:
  `export MAGICK_HOME=$HOME/ImageMagick`
  `export PATH=$MAGICK_HOME/bin:$PATH`
  `export DYLD_LIBRARY_PATH=$MAGICK_HOME/lib/`

- 8a) # check configuration:
  `convert -list configure`

- 8b) # check image format supported:
  `identify -list format`

- Tips:
  Prior to 4), please make sure `libjpeg` and `libpng` are installed. If NOT, for Mac try this:
  `brew install libjpeg libpng librsvg`
  To check whether ImageMagick does work, please get additional information from:
  `identify -list format`
  `convert -list configure`
  On details, please refer to http://www.imagemagick.org/script/advanced-unix-installation.php

### See Also

`visNetMul`

### Examples

    ## Not run:
    library(XGR)

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
    ## Not run:
    g <- erdos.renyi.game(20, 1/10)
    glayout <- layout_with_kk(g)
    ls_xyz <- data.frame(x=glayout[,1], y=glayout[,2], z=degree(g),
    label=degree(g))

    # 3D views of different angles
    # output as a pdf file
    xVisInterpAnimate(ls_xyz, image=TRUE, filetype="pdf")
    # output as a mp4 file
    xVisInterpAnimate(ls_xyz, filetype="mp4")
    # output as a gif file
    xVisInterpAnimate(ls_xyz, filetype="gif", num.frame=72,
    sec_per_frame=0.5)

    ## End(Not run)