\name{geneAnnotationHeatmap} \alias{geneAnnotationHeatmap} %- Also NEED an '\alias' for EACH other topic documented here. \title{ Make a concept-gene cross tabulation } \description{ Function to make a concept-gene cross tabulation } \usage{ geneAnnotationHeatmap(annotationList, dataMatrix = NULL, addGeneLabel = TRUE, colorMap = c("#000000", "#FFFFFF"), sortBy = "both", standardize.data = TRUE, colorMap.data = "GBR", sortBy.data = "row", mar = c(1, 1, 8, 6), cex.axis = c(0.8, 0.8), mapType = c("table", "heatmap"), displayAll=FALSE, ...) } %- maybe also 'usage' for other objects documented here. \arguments{ \item{annotationList}{ a list of annotation to gene mapping. } \item{dataMatrix}{ a 2-dimensional numeric matrix. If it is provided, it will be plot side by side with the annotation heatmap. } \item{addGeneLabel}{ logic, indicate whether add gene labels } \item{colorMap}{ vector to specify color map of the two-color annotation heatmap } \item{sortBy}{ string to specify whether to sort the annotation matrix by row, column, both row and column or none of them } \item{standardize.data}{ logic, specify whether to standardize the dataMatrix by row~~ } \item{colorMap.data}{ string to specify color map of the dataMatrix heatmap } \item{sortBy.data}{ string to specify whether to sort the dataMatrix by row, column, both row and column or none of them } \item{mar}{ integer vector to speicify margin of the plot } \item{cex.axis}{ integer vector to specify the character size of row and column labels } \item{mapType}{string to specify concept-gene map type} \item{displayAll}{logic, specify to show all of gene expression profile or remove redundant entries.} \item{\dots}{ other parameters used by .heatmap.mds } } \details{ 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". } \value{ The function will generate a map without return value. } \author{ Pan Du, Gang Feng and Simon Lin } \seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ } \examples{ 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') \dontrun{geneAnnotationHeatmap(a,dataMatrix=b)} } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. \keyword{ methods }