# plotBM: Visualization of a binary matrix In Ringo: R Investigation of ChIP-chip Oligoarrays

## Description

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

## Usage

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

## Arguments

 `x` Binary matrix to visualize `boxCol` Color to use for boxes of '1's `reorder` logical; states whether the rows shall be reordered according to the size of the category `frame` logical; states whether a frame should be drawn around the visualization. In contrast to the frame drawn in `plot.default`, there is no gap between the visualization and this frame. `...` further arguments passed on to `plot.default`

## 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

`polygon`,`colors`

## Examples

 ```1 2 3 4 5 6``` ``` 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) ```

### Example output

```Loading required package: Biobase

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':

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

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, 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")'.

Attaching package: 'limma'

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

plotMA

Warning message:
URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
I II III IV
a 0  0   1  0
b 0  1   1  0
c 1  0   1  0
d 1  0   0  1
e 1  0   0  0
f 1  1   0  1
g 1  0   0  1
h 0  0   1  1
i 0  0   0  0
j 1  0   0  1
k 1  1   1  1
l 1  1   0  0
m 0  1   0  1
n 0  0   1  0
o 1  0   0  0
p 0  1   1  0
q 0  1   0  0
r 0  1   1  0
s 0  1   1  0
t 1  1   1  0
```

Ringo documentation built on May 2, 2018, 4:13 a.m.