makeGGV {iGenomicViewer} | R Documentation |
This functions acts on a GGV 'generic genomic viewer' object to create a series of interactive plots.
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)
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 |
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.
A series of interactive plots are generated within the given directory, dir
see vignette for more details
Lori A. Shepherd
# see vignette for example