matrixPlot: Basic plot function for IBD segments

In hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

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)

hapFabia documentation built on Nov. 8, 2020, 5:17 p.m.