makeGGV {iGenomicViewer}R Documentation

Creates a Series of Interactive Plots

Description

This functions acts on a GGV 'generic genomic viewer' object to create a series of interactive plots.

Usage

makeGGV(GGV,
        goodDX=NA,
        smplDX=NA,
        smp.color=NA,
        break.num=125,
        tileNum = 2, 
        buffer = 5,
        makeWinArms=TRUE, 
        tiledMat=NA,
        tiledMai.mat = NA,
        tiledMai.prc=FALSE,
        fname.root="iGGV",
        dir="GGV/",
        overwriteSourcePlot = NA,
        header="v3",
        window.size = "800x1100",
        image.size = "800x1100",
        tiled.window.size = "800x1100",
        tiled.image.size = "1200x1100",
        cleanDir = TRUE)

Arguments

GGV a GGVobj, 'generic genomic viewer' object
goodDX range of acceptable y values. This is used as a way to removed spots of known bad quality. should correspond to locations in the mapObj$mapping.info object
smplDX index or ordering for x axis
smp.color colors for x axis
break.num numeric indicating break lengths to break up heatmap for interactivity
tileNum For tiled image heatmaps, the number of tracks to split spot.IDs
buffer An additional number of spots to plot surrounding know regions.
makeWinArms Should within Arm sub plots be generated. This creates all chromosome sub plots for chromosomes listed
tiledMat 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. This matrix will be used for tiled images only. mat for chromosome arms and sub arms are specified in initGGV
tiledMai.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. This will be used for tiled images only. mai.mat for chromosome arms and sub arms are specified in initGGV
tiledMai.prc logical indicating if mai mat values are percentages or hard coded values. If mai.prc is T, indicates percentage. This will be used for tiled images only. mai.prc for chromosome arms and sub arms are specified in initGGV
fname.root Base name to use for index file and genomic plot if applicable.
dir directory path to where files and sub directories should be created
overwriteSourcePlot character, should static image generated be a postscript, png, jpeg, or tiff. 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 for chromosome arm and sub chromosome arm plots. see makeSplot for more details
image.size character indicating resize value of image,'width'x'height' for chromosome arms and sub chromosome arm plots. see initSplot for more details
tiled.window.size size of the html window for tiled image plots.see makeSplot for more details
tiled.image.size character indicating resize value of image,'width'x'height' tiled image plots. see initSplot for more details
cleanDir logical indicating if temporary files should be removed

Details

see vignette for better details

This function creates a series of plots based on user settings. The top layer is a chromosome arm index page with listed arms in chrArms. If a genomic plot is specified in the GGVobj$values$plot.call, a genomic plot is also generated for the given subregion (based on GGVobj$values$plot.dx, GGVobj$values$plot.vec). While the initial plot will be plotted over the given plot.dx, it is important that the plot.vec and plot.call arguments are across the genome so the plot may be included on any chromosome arm plots specified. The next set of plots are the chromosome arm plots with limit interactivity. These plots will be generated for all chromosome arms listed in chrArm or utilized in the genomic plot plot.dx. The main heatmap is not interactive in these plots, only the annotation tracks and, if applicable, the genomic plot are interactive. Additional annotation tracks for known regions of interest as well as sub chromosome arm regions are added. The known regions are tiled image displays; these regions were specified in GGV$values$trackRegions. see makeTrack. If the user clicks on one of these regions the assocaited plot will appear. The sub chromosome arm regions are fully interactive plots. These plots are only generated if makeWinArms is TRUE. If makeWinArms is FALSE the links in these regions will not work properly.

Value

A series of interactive plots are generated within the given directory, dir

Note

see vignette for more details

Author(s)

Lori A. Shepherd

See Also

GGVobj,initGGV

Examples


# see vignette for example


[Package iGenomicViewer version 2.4.6 Index]