TIplot-class {iGenomicViewer}R Documentation

TIplot 'tiled image' class

Description

The tiled image object contains all necessary information to plot a tiled image heatmap. This includes but is not limited to matrix of values, axis ranges, axis labels, size, and mapping information.

TIplot structure

tractBound
The tractBound object contains all information for breaking up the yaxis spot list into different tracks. For detailed information please see vignette
vls
The vls list contains information on values for plotting. There is a matrix or start and stop genomic locations for the y axix, Y. There is also the matrix of values, Z. The object H is a numeric indicating the number of tracks to break each sample into. Xcoords is a numeric list indicating each tracks x value. Finally nsmp and nBAC indicate the number of samples and the number of spots used. For more detail see vignette.
lims
The lims list contains vectors of the range for the xaxis, yaxis and Z matrix [xlim, ylim, zlim]
labels
The labels list contains values for individual x labels and ylabels, as well as labels for title, xaxis and yaxis. [ttl, xlab, ylab]
Zcol
Zcol is a vector of colors for the Z matrix scale
cex
The cex, or size, list consists of the x axis and y axis values for point size, given as xcex and ycex respectively
map
The map list consists of the spot ID index [bacDX] and the associated mapping object [mapObj]. Please see mapobj for details on this structure

Note

Users are encouraged to view the vignette for more detail

Author(s)

Lori A. Shepherd, Daniel P. Gaile

See Also

initTiled


[Package iGenomicViewer version 2.4.6 Index]