geneAnnotationHeatmap: Make a concept-gene cross tabulation
In GeneAnswers: Integrated Interpretation of Genes

Description Usage Arguments Details Value Author(s) References Examples

Function to make a concept-gene cross tabulation

geneAnnotationHeatmap(annotationList, dataMatrix = NULL, addGeneLabel = TRUE, colorMap = c("#000000", "#FFFFFF"), sortBy = "both", standardize.data = TRUE, colorMap.data = "default", showGeneMax = 200, sortBy.data = "row", mar = c(1, 1, 8, 6), cex.axis = c(0.8, 0.8), mapType = c("table", "heatmap"), displayAll=FALSE, symmetry=FALSE, colorBar=FALSE, colorBarLabel=NULL)

`annotationList`	a list of annotation to gene mapping.
`dataMatrix`	a 2-dimensional numeric matrix. If it is provided, it will be plot side by side with the annotation heatmap.
`addGeneLabel`	logic, indicate whether add gene labels
`colorMap`	vector to specify color map of the two-color annotation heatmap
`sortBy`	string to specify whether to sort the annotation matrix by row, column, both row and column or none of them
`standardize.data`	logic, specify whether to standardize the dataMatrix by row~~
`colorMap.data`	string to specify color map of the dataMatrix heatmap
`showGeneMax`	an integer, the maximum of gene number to show genes id or symbol on the heatmap
`sortBy.data`	string to specify whether to sort the dataMatrix by row, column, both row and column or none of them
`mar`	integer vector to speicify margin of the plot
`cex.axis`	integer vector to specify the character size of row and column labels
`mapType`	string to specify concept-gene map type
`displayAll`	logic, specify to show all of gene expression profile or remove redundant entries.
`symmetry`	logic, indicate the values corresponding to two extreme colors are same if TURE.
`colorBar`	logic, show colorbar or not
`colorBarLabel`	character vector to show color bar label.

This function basically generates two maps in one canvas. Left side is a heatmap based on given expression matrix. Right side is a concept-gene map, which could be represented as two-color heatmap or table, depends on parameter "mapType".

The function will generate a map without return value.

Pan Du, Gang Feng and Simon Lin

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

a <- list(group1 = c('a','b','c','d','f'), group2= c('b','d','e','a','g','h'))
b <- matrix(rnorm(48), nrow=8,ncol=6)
rownames(b) <- tolower(LETTERS[1:8])
colnames(b) <- c('ctrl1', 'ctrl2', 'ctrl3', 'treat1', 'treat2', 'treat3')
## Not run: geneAnnotationHeatmap(a,dataMatrix=b)

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: RSQLite
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

Loading required package: Heatplus
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers' 
2: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'