plotHeatmap: Plot heatmaps

Description

A function to plot heatmaps

Usage

"plotHeatmap"(object,bins=100,col=heat.colors(100), 
rowScale=TRUE,orderPosition=NULL,orderBy="maxAtPosition",...)
"plotHeatmap"(object = "ChIPprofile", bins = 100, col = heat.colors(100), rowScale = TRUE, orderPosition = NULL, orderBy = "maxAtPosition", ...)

Arguments

object

A ChIPprofile object

bins

Numeric vector of number of bins to summarise columns over (Useful for full resolution "profile" styles). Default is 100. Set to NULL for no binning to be performed Useful for comparing multiple samples of differing depths without normalisation. Default is FALSE.

col

Colour scale to use for heatmap.

rowScale

TRUE or FALSE. Perform row centering and scaling. Default is TRUE.

orderPosition

Numeric vector of positions used for sorting when orderBy is set to "maxAtPosition". May be single value specifying index for ordering or vector of numeric values where maximum and minimum index positions specify an index range used for sorting.

orderBy

Character specifing method for heatmap row ordering. At present only "maxAtPosition".

...

Additional arguments passed to image() maxAtPosition method - Order heatmap by score at index specified in orderPosition. Ordered from maximum to minimum.

Value

A matrix of values displayed in heatmap

Examples

Run this code

data(chipExampleBig)
plotHeatmap(log(chipExampleBig),orderPosition=c(100:200),bins=NULL,col=topo.colors(100))

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