iGGVtiled {iGenomicViewer} | R Documentation |
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.
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, ...)
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 |
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.
.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.
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.
Lori A. Shepherd, Daniel P. Gaile
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")