Make a concept-gene cross tabulation

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Description

Function to make a concept-gene cross tabulation

Usage

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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)

Arguments

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.

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(s)

Pan Du, Gang Feng and Simon Lin

References

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

Examples

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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)

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