| matrixPlot {hapFabia} | R Documentation |
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.
matrixPlot(x,range=NULL,yLabels=NULL,zlim=NULL,title=NULL,colRamp=12,grid=FALSE,pairs=FALSE,padj=NA,...)
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. |
Implementation in R.
Plots a matrix where different values are coded by different colors
Sepp Hochreiter
S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.
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
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)