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]