geneAnnotationHeatmap {GeneAnswers} | R Documentation |
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)