initTile {iGenomicViewer}R Documentation

Creates A Tiled Display Image 'TIplot' Object

Description

The initTile function creates a tiled display image 'TIplot' object. A TIplot object holds all necessary elements to make a tiled display plot.

Usage

initTile(Z,
         bacDX,
         goodDX=NA,
         mapObj=NA,
         H=2,
         zlims=c(-0.5,0.5),
         smplDX=NA,
         ylabels=NA,
         xlabels=NA,
         x.axis.cex =0.5,
         y.axis.cex =0.5,
         xlab="samples",
         ylab="BAC location",
         ttl=NA,
         returnVl=TRUE,
         saveFlag=FALSE,
         saveName="TIplot.RData")

Arguments

Z matrix of values for image. The number of rows and columns should be equal to the lenghts of bacDX and smplDX. If the matrix is larger the matrix will be subset based on bacDX and smplDX
bacDX index of spot.ID's to graph. should correspond to index in mapObj. This will be used to determine the genomic start and stopping location of the plot
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
mapObj an object of the class mapobj. This object should be made with genomic starting and stopping locations not a central location
H number of tracks to display per sample
zlims minimum and maximum range for values in Z
smplDX subset for x axis. If the second dimension of Z is larger than or equal to the length of smplDX, Z will be subset based on this index
ylabels vector indicating labels for Y axis. Should be equal in length to the number of rows in Z [or Y]
xlabels vector indicating labels for X axis. Should be equal in length to the number of columns in Z
x.axis.cex display size of xlabels
y.axis.cex display size of ylabels
xlab main x axis label for plot
ylab main y axis label for plot
ttl main title for plot
returnVl Should TIplot object be returned
saveFlag Should TIplot object be saved
saveName If saveFlag, path file name to save object

Details

The initTile function creates a tiled display image 'TIplot' object. A TIplot object holds all necessary elements to make a tiled display plot. The function takes in a matrix of values to display as a tiled image, Z,and a bacDX indicating the spot.IDs that should be used and correspond to the rows of Z. If Z has more rows than the length of bacDX, it is assumed that Z should be subset based on bacDX. The bacDX should refer to spot.IDs given in a mapObj. If no mapObj is used, the default package mapObj is used. It is also possible to subset Z based on a smplDX. If no smplDX is given it is assumed that all columns of Z should be used. 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.

Value

If returnVl, an object of the class 'TIplot'

Note

Assumes genomic location values on Y axis and samples on X axis

Author(s)

Lori A. Shepherd, Daniel P. Gaile

See Also

convertLoc, TIplot, makeTile, iGGVtiled

Examples


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")


[Package iGenomicViewer version 2.4.6 Index]