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hapFabia (version 1.14.0)

matrixPlot: 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.

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

Run this code

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)

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