Plotting of Genomic Data

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

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 <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(idiogram)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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 objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: plotrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/idiogram/idiogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: idiogram
> ### Title: Plotting of Genomic Data
> ### Aliases: idiogram midiogram
> ### Keywords: hplot
> 
> ### ** 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.")
Loading required package: hu6800.db
Loading required package: org.Hs.eg.db


Loading required package: golubEsets
> 
> ## 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")
Warning: zlim used is:  -0.839888 0.787702  Please see  'dlim'  to adjust.
> 
> idiogram(colo.eset,ucsf.chr,chr="1",method="image",col=topo.colors(50),grid.lty=c(1,NA))
Warning: zlim used is:  -0.839888 0.787702  Please see  'dlim'  to adjust.
> 
> 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)
+ }
There were 12 warnings (use warnings() to see them)
> 
> par(op)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>