heatmapCombinations: Plot a heatmap of combinatorial states

Description

Plot a heatmap that shows the binary presence/absence of marks for the different combinations.

Usage

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heatmapCombinations(model = NULL, marks = NULL, emissionProbs = NULL)

Arguments

model

A multiHMM object or file that contains such an object.

marks

A character vector with histone marks. If specified, model will be ignored.

emissionProbs

A matrix with emission probabilities where dimnames(emissionProbs) gives the state labels and marks. This option is helpful to plot probabilistic chromatin states (not part of chromstaR). If specified, model and marks will be ignored.

Value

A ggplot object.

Author(s)

Aaron Taudt

See Also

plotting

Examples

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marks <- c('H3K4me3','H3K27me3','H4K20me1')
heatmapCombinations(marks=marks)

file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
heatmapCombinations(file)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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