geneAnnotationHeatmap {GeneAnswers} | R Documentation

## 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 = "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

    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)

[Package GeneAnswers version 2.26.0 Index]