matrixPlot {hapFabia} | R Documentation

## Basic plot function for IBD segments

### Description

`matrixPlot`: R implementation of `matrixPlot`.

Plots a matrix where different values are coded by different colors. Basically the image plot function `image` with a particular scaling, color coding, and axis.

### Usage

    matrixPlot(x,range=NULL,yLabels=NULL,zlim=NULL,title=NULL,colRamp=12,grid=FALSE,pairs=FALSE,padj=NA,...)

### Arguments

`x` | matrix that codes alleles and annotations of an IBD segment.
`range` | optional: physical range of the IBD segment.
`yLabels` | optional: labels of the individuals.
`zlim` | optional: limits imposed onto the matrix values.
`title` | title of the plot.
`colRamp` | color representation.
`grid` | does the plot have a grid?; default FALSE (no).
`pairs` | for pairwise groups, e.g. case-control, twins, etc.; default FALSE (no).
`padj` | adjustment for each tick label perpendicular to the reading direction.
`...` | other graphical parameters may also be passed as arguments to this function.

### Details

Implementation in R.

### Value

Plots a matrix where different values are coded by different colors

### Author(s)

Sepp Hochreiter

### References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

### See Also

`IBDsegment-class`, `IBDsegmentList-class`, `analyzeIBDsegments`, `compareIBDsegmentLists`, `extractIBDsegments`, `findDenseRegions`, `hapFabia`, `hapFabiaVersion`, `hapRes`, `chr1ASW1000G`, `IBDsegmentList2excel`, `identifyDuplicates`, `iterateIntervals`, `makePipelineFile`, `matrixPlot`, `mergeIBDsegmentLists`, `mergedIBDsegmentList`, `plotIBDsegment`, `res`, `setAnnotation`, `setStatistics`, `sim`, `simu`, `simulateIBDsegmentsFabia`, `simulateIBDsegments`, `split_sparse_matrix`, `toolsFactorizationClass`, `vcftoFABIA`

### Examples

    mat <- matrix(0,nrow=10,ncol=40)
    v1 <- sample(1:10,5)
    v21 <- sample(1:40,4)
    v22 <- sample(1:40,4)
    w1 <- rep(0,10)
    w2 <- rep(0,40)
    w1[v1] <- 1
    w2[v21] <- 1
    w2[v22] <- 2
    mat <- mat + tcrossprod(w1,w2)

    matrixPlot(mat)

[Package hapFabia version 1.26.0 Index]