GGVobj-class {iGenomicViewer}R Documentation

GGV 'generic genomic viewer' class

Description

The generic genomic viewer object contains all necessary information to plot a series of interactive genomic plots.

GGVobj structure

values
Contains values, objects, and matricies with main data source
interactive
contains matricies and vectors of interactive data for the plots
info
contains values of other arguments used in functions call

GGVobj's values structure

vls
a matrix of values for the heatmap. assumes full set do not subset based on plot.x.index or plot.y.index, the function will automatically subset. The number of rows should correspond to the number of spot IDs in the mapObj
mapObj
an object of the class mapobj
annObj
an annotation object
chrArms
Character vector of chromosome arms to be plotted. These names should match arm names in the mapObj's band.info. These Chromosomes will be diplayed in an index file
trackRegions
A list containing character vectors for Broad.Band, Fine.Band, and geneName. Also may contain a n by 2 matrix of genomic start and stop values. These are known regions of interested that will be displayed as tiledImages. See makeTrack
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. This matrix will be used for Chromosome Arm and Sub.Arm Plots
plot.call
character vector containing extra plotting calls that will be evaluated on the optional side plot. 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.
plot.vec
vector of values that will be plotted in the side plot. If NA, no plot will be added to the display. These values are the additional plots x-values. See details
plot.dx
Index to subset plot.vec on when creating an initial genomic plot. If NA, all values are used

GGVobj's interactive structure

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.

GGVobj's info structure

maxLabels
maximum number of labels to appear on the heatmap y axis
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. This will be used for Chromosome Arm and Sub.Arm plots
mai.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 Chromosome Arm and Sub.Arm plots
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 entry must be a character vector. If no additional plotting is equired, an NA should be used
smpLines
logical indicating if vertical lines should be added between each sample of the heatmap
divCol
If smpLines, the color of the dividing lines
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 track
mapObj.columns
Which columns from mapObj's mapping.info data.frame to include in tool-tip. May be numeric or header names

Note

Users are encouraged to view the vignette for more detail

Author(s)

Lori A. Shepherd

See Also

makeGGV, initGGV, updateGGV


[Package iGenomicViewer version 2.4.6 Index]