matrixPlot: Basic plot function for IBD segments

Description Usage Arguments Details Author(s) References See Also Examples

View source: R/hapFabia.R

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

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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.

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

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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)

Bioconductor-mirror/hapFabia documentation built on June 1, 2017, 10:40 a.m.