Visualization of a binary matrix

Description

This function produces simple, heatmap-like visualizations of binary matrices.

Usage

plotBM(x, boxCol = "darkblue", reorder = FALSE, frame = TRUE, ...)

Arguments

Details

For reordering, each row is interpreted as a binary matrix, for example a row z=(1,0,0,1) would be interpreted as the binary number 1001 = 9 in the decimal system. Rows are then reordered by the frequency of each binary number with the rows that correspond to the most frequent binary number shown at the top in the visualization.

Value

The function invisibly returns the (reordered) matrix x, but its mainly called for its side effect of producing the visualization.

Note

An alternative way to display such matrices are given by heatmap or, the simpler version thereof, image. However, image files produced with this functions tend to be very large. This function uses plot.default and polygon which results in much smaller file sizes and is sufficient for binary matrices.

Author(s)

Joern Toedling

See Also

polygon,colors

Examples

  A <- matrix(round(runif(80)), ncol=4, byrow=TRUE)
  dimnames(A)=list(letters[seq(nrow(A))],
                   as.character(as.roman(seq(ncol(A)))))
  show(A)
  plotBM(A, reorder=FALSE)
  plotBM(A, reorder=TRUE)

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(Ringo)
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: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/plotBM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBM
> ### Title: Visualization of a binary matrix
> ### Aliases: plotBM plotBinaryMatrix
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   A <- matrix(round(runif(80)), ncol=4, byrow=TRUE)
>   dimnames(A)=list(letters[seq(nrow(A))],
+                    as.character(as.roman(seq(ncol(A)))))
>   show(A)
  I II III IV
a 1  1   0  0
b 0  1   1  0
c 1  0   1  0
d 1  1   0  1
e 1  1   0  1
f 0  1   1  0
g 0  0   0  0
h 1  1   1  1
i 1  0   1  1
j 0  1   1  1
k 1  1   0  0
l 0  0   1  0
m 0  1   1  1
n 0  1   0  0
o 1  1   0  0
p 1  0   1  0
q 0  1   1  0
r 0  0   1  0
s 1  1   1  0
t 0  0   0  0
>   plotBM(A, reorder=FALSE)
>   plotBM(A, reorder=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>