idiogram: Plotting of Genomic Data

In idiogram: idiogram

Description

Function for plotting genomic data along with corresponding cytogenetic banding information

Usage

idiogram(data, genome, chr=NULL, organism=NULL,
method=c("plot","matplot","image"), margin=c("ticks","idiogram"),
grid.col=c("red","grey"), grid.lty=c(1,2), widths=c(1,2),
relative=FALSE, dlim=NULL, main=NA, xlab=NA,
ylab=NA,cex.axis=.7,na.color = par("bg"),cen.color="red", mb=FALSE,
...)

Arguments

data	a vector or matrix of numeric data to plot. The names/rownames attribute needs to contain corresponding gene identifiers
genome	a chromLocation object associated with the specified data set. See below for details.
chr	which chromosome to plot
organism	if NULL, determination of the host organism will be retrieved from the organism slot of the chromLocation object. Otherwise "h", "r", or "m" can be used to specify human, rat, or mouse chromosome information
method	plotting method
margin	type of banding information to display in the plot margin
grid.col	a two element vector specifying the centromere and band grid colors.
grid.lty	a two element vector specifying the centromere and band grid line type.
widths	a two element vector specifying the relative width of the margin idiogram two the adjacent graph. This option is currently ignored.
relative	If relative is TRUE, the vertical height of the plot is scaled relative to the size of largest chromosome.
dlim	a two element vector specifying the minimum and maximum values for x. Data in x that exceed the min and max limits will be set to the min/max limit values before plotting.
main	an overall title for the plot. Defaults to the chromosome name.
xlab	a title for the x axis.
ylab	a title for the y axis.
cex.axis	the magnification to be used for axis annotation relative to the current.
na.color	color to be used for NA values, defaults to: par("bg")
cen.color	color to be used for the centromere when margin="idiogram", defaults to: "red"
mb	if TRUE, subset data to include just those row names starting with the value of the argument chr. Otherwise, use chromLoc as outlined below.
...	additional graphical parameters can be given as arguments.

Details

This function displays cytogenetic banding information in the plot margin and calls a secondary plotting function to display associated data at the same relative position. Cytogenetic data for human, mouse, and rat genomes are currently included.

The data is arranged by associating gene identifiers to genomic location using a chromLoc annotation object built using the buildChromLocation function from the annotation package. As such, a vector of data is to be plotted, the names attribute of the vector needs to contain the gene identifiers. Likewise if a matrix of data is to be plotted, the rownames attribute of the matrix needs to contain the gene identifiers.

To date, plot can be called for vector data, while matplot and image can be called for matrix data. Most additional plotting arguments can be passed down via .... However, the idiogram function plots the axis independently. Currently, only the cex.axis,col.axis, and font.axis parameters are intercepted from ... and redirected to the specialized axis call. Other parameters that effect the axis should be set via par.

The function midiogram is a simple wrapper around idiogram to plot all the chromosomes from a particular organism using sensible default values. The "m" refers to plotting multiple idiograms.

Author(s)

Kyle Furge <[e-mail]> and Karl Dykema <[e-mail]>

See Also

buildChromLocation, Hs.cytoband, idiograb

Examples

library(idiogram)

## 
## NOTE:This requires an annotation package to work.
##      In this example packages "hu6800.db" and "golubEsets" are used.
##      They can be downloaded from http://www.bioconductor.org
##      "hu6800.db" is under MetaData, "golubEsets" is under Experimental
##      Data.


if(require(hu6800.db) && require(golubEsets)) {
   library(golubEsets)
   data(Golub_Train)

   hu.chr <- buildChromLocation("hu6800")
   ex <- assayData(Golub_Train)$exprs[,1]

   ## make sure the names() attribute is set correctly
   gN <- names(ex)
   gN[1:10]   

   idiogram(ex,hu.chr,chr="1")

   colors <- rep("black",times=length(ex))
   colors[ex > 10000] <- "red"
   pts <- rep(1,times=length(ex))
   pts[ex > 10000] <- 2
   idiogram(ex,hu.chr,chr="1",col=colors,pch=pts,font.axis=2,cex.axis=1)
   abline(v=0,col="darkgreen")

   ## An example of the dlim option. It is most useful for making
   ## consistant multi-panel plots
   colors <- rep("black",times=length(ex))
   colors[ex > 10000] <- "red"
   colors[ex < 0] <- "blue"

   idiogram(ex,hu.chr,chr="1",col=colors,xlim=c(-3000,21000))
   idiogram(ex,hu.chr,chr="1",col=colors,dlim=c(-100,7500),xlim=c(-3000,21000))
   idiogram(ex,hu.chr,chr="1",col=colors,dlim=c(-100,7500),xlim=c(-3000,10000))

   ## Using the identify function
   ip <- idiogram(ex,hu.chr,chr="1",col=colors,pch=19)
   #identify(ip$x,ip$y,labels=ip$labels)
   
} else print("This example requires the hu6800.db and golubEsets data packages.")

## The example data is BAC array CGH data from J. Fridlyand's
## aCGH package

data(idiogramExample)

idiogram(colo.eset[,1],ucsf.chr,chr="1")

idiogram(colo.eset,ucsf.chr,chr="1",method="image")

idiogram(colo.eset,ucsf.chr,chr="1",method="image",col=topo.colors(50),grid.lty=c(1,NA))

idiogram(colo.eset,ucsf.chr,chr="1",method="mat",type="l")

## for a consistant multi-panel plot it can be helpful to force the data
## range within each panel to a defined range using 'dlim'
## This is similar to calling the 'midiogram' function

op <- par(no.readonly=TRUE)
par(mai=par("mai")*c(0.1,0.5,0.5,0.5))
layout(rbind(c(1:8),c(0,9:14,0),c(15:22)))

for(i in c(1:22)) {
  idiogram(colo.eset,ucsf.chr,chr=i,method="i",dlim=c(-1,1),margin="i",relative=TRUE)
}

par(op)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: plotrix
Loading required package: hu6800.db
[1] "This example requires the hu6800.db and golubEsets data packages."
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'hu6800.db'
Warning: zlim used is:  -0.839888 0.787702  Please see  'dlim'  to adjust.
Warning: zlim used is:  -0.839888 0.787702  Please see  'dlim'  to adjust.
There were 12 warnings (use warnings() to see them)

idiogram documentation built on Nov. 8, 2020, 5:54 p.m.