iGGVtiled {iGenomicViewer}R Documentation

Interactive Tiled Display

Description

This function takes a tiled image display 'TIplot' object and creates an interactive layout of plots. The tiled display will be the main plot of the layout.

Usage

iGGVtiled(TIplot,
          annObj,
          x.labels=NA,
          y.labels=NA,
          xy.labels=NA,
          x.links=NA,
          y.links=NA,
          xy.links=NA,
          asLinks=NA,
          x.images=NA,
          y.images=NA,
          xy.images=NA,
          mat=NA,
          mai.mat = NA,
          mai.prc=FALSE,
          plot.extras=NA,    
          smpLines=TRUE,
          divCol="lightgrey",
          plot.call=NA,
          plot.vec=NA,
          lims = c(-0.5,0.5),
          annotation = NA,
          clrs=c("blue", "hotpink", "purple", "orange"),
          mapObj.columns = NA,
          fname.root="iGGV",
          dir="./",
          overwriteSourcePlot = NA,
          makeInteractive=TRUE,
          overrideInteractive=NA,
          header="v3",
          window.size = "800x1100",
          image.size= "800x1100",
          cleanDir=TRUE,
          vrb=TRUE,
          ...)

Arguments

TIplot an object of the class TIplot. This object's genomic locations must be with respect to the entire genome not location within chromosome.
annObj an annotation object
x.labels data frame of n x m which contains values relating to the x-axis values. This information is displayed in the interactive plot window.
y.labels data frame of n x m which contains values relating to the y-axis values. This information is displayed in the interactive plot window.
xy.labels list of matricies. All matricies should be of n x m. This information is displayed in the interactive plot window.
x.links data frame of n x m which contains web addresses for links relating to the x-axis values. This information is displayed as hyperlinks in the interactive plot window.
y.links data frame of n x m which contains web addresses for links relating to the y-axis values. This information is displayed as hyperlinks in the interactive plot window.
xy.links list of matricies. All matricies should be of n x m. This information is displayed in the interactive plot window as hyperlinks. The values in these matricies should be complete web address.
asLinks contains complete web address for points that should be treated as hyperlinks.
x.images data frame of n x m which contains paths to images relating to the x-axis values. This information is displayed as images in the interactive plot window.
y.images data frame of n x m which contains paths to images relating to the y-axis values. This information is displayed as images in the interactive plot window.
xy.images list of matricies. All matricies should be of n x m. This information is displayed in the interactive plot window as images. The values in these matricies should be complete paths to images.
mat matrix indicating layout. This argument will be passed into the graphics package layout call as mat.Each value in the matrix must be '0' or a positive integer. If N is the largest positive integer in the matrix, then the integers {1,...,N-1} must also appear at least once in the matrix. '0' indicates region of no plotting. This may be left as NA, and a default will be used
mai.mat n x 4 matrix of values to be passed in for each plots par mai. n will be 3 if plot.call is NA, and 4 if plot.calls is specified
mai.prc logical indicating if mai mat values are percentages or hard coded values. If mai.proc is T, indicates percentage.
plot.extras List of length equal to the number of plots: 3 if plot.call is NA, 4 if plot.call is specified. This object is a list of lists. The sublists contain any additional plotting calls that should be executed for the plot. Each ntry must be a character vector. If no additional plotting is equired, an NA should be used
smpLines logical indicating if vertical, yellow lines should be added between each sample of the heatmap.
divCol If smpLines, the color of the dividing lines
plot.call character vector containing plot call that will be evaluated. This plot is added to the right of the annoation tracks. It is designed to add additional statistical analysis such as p.values, linear order statistics, etc. If NA, no plot will be added to the display
plot.vec vector of values that will be plotted in plot.call. While this may be specified in the plot.call, it is also necessary in order to add interactive tool-tip to values
lims Lower and Upper limit for vls
annotation Numeric indication of which annotation information objects to include from the annObj. If NA all are used.
clrs Character vector of colors to use for annotation tracks
mapObj.columns Which columns from mapObj's mapping.info data.frame to include in tool-tip. May be numeric or header names
fname.root Base name to use for all file created
dir directory path to where files should be created
overwriteSourcePlot character, should static image generated be a postscript, png,jpeg, or tiff. see makeSplot for more details
makeInteractive logical, should interactive html file be created.see makeSplot for more details
overrideInteractive Indicates which figures of the layout should be interactive. see makeSplot for more details
header May either be v1,v2, or v3. Determines which tooltip header will be in the html file. see makeSplot for more details
window.size size of the html window. see makeSplot for more details
image.size character indicating resize value of image,'width'x'height' see initSplot for more details
cleanDir logical indicating if intermediate files created for mapping purposes should be deleted
vrb logical indicating if status messages should be printed
... extra arguments to makeImap function

Details

This function is a wrapper to sendplot to create an interactive bioinformatics heatmap display.

The main plot of the layout is a tiled display image. The reasoning behind the tiled image is that there are spot.ID, BAC clones, etc. that span the genome. The different regions may overlap or not include certain regions across the entire genome. This viewer breaks the spot.IDs to show how they are covering a particular region.

This function requires an object of the class TIplot, a mapping object, and an annotation object. For details on creating the mapping and annoation objects see mappingObj and annotation. For details on creating the TIplot object see initTile. The TIplot start and stop genomic locations must be with respect to the entire genome not with chromosome. If the TIplot object was created with the later, plese see convertLoc for help on converting these locations and recreate the object.

It is possible to control what is displayed from the annotation object so that any, all, or none of the annotation information may be displayed as tracks along side the heatmap. The annotation argument is a numeric corresponding to the order of the annotation information objects in the annObj. NA will display all. 0 will display none.

For more details on interactive plotting capabilities, please refer to vignette.

Value

.png [.jpeg,.ps] and .html graphs. .html is an interactive display. The display will have a tiled heatmap, legend, annotation track, and, if utilized, an extra descriptive plot.

Note

Works properly on linux/unix operating systems only.

The TIplot object must have Y locations with respect to entire genome not within chromosome. See convertLoc for conversion option.

Author(s)

Lori A. Shepherd, Daniel P. Gaile

See Also

initTile,makeTiled, iGGV

Examples


library("iGenomicViewer")

# load data objects
data(iGGVex)
data(mapping.info)
mapObj = mapping.info

# create a subset range
bacDX = 103:112
smplDX = 1:10
Z = mat[bacDX,smplDX]

# make object
TIplot = initTile(Z=Z,
                  bacDX=bacDX, mapObj=mapObj,
                  H=3,zlims=c(-0.5,0.5),
                  ylabels=paste("Spot",bacDX, sep=""),
                  xlabels=paste("smp",smplDX, sep=""),
                  xlab="Samples",
                  ylab="SpotID",
                  ttl="tiledImage",
                  returnVl=TRUE,
                  saveFlag=FALSE,
                  saveName="TIplot.RData")

# annotaiton object
# see vignette and help files for more details
data(annObj)

# make interactive plot

iGGVtiled(TIplot=TIplot,
          annObj=annObj,
          x.labels=as.data.frame(list(
                  sample.ID=paste("smp",1:TIplot$vls$nsmp,sep=""),
                  xla1=c("a","b","c","d","e","f","g","h","i","j"),
                  xla2=10:1)),
          y.labels=as.data.frame(list(
                  Spot.ID=paste("Spot",bacDX,sep=""))),
          xy.labels=list(lgr=round(Z,3)),
          mapObj.columns = c(2,3,7),
          fname.root="iGGVtiled")

   
  



[Package iGenomicViewer version 2.4.6 Index]