heatmapTransitionProbs: Heatmap of transition probabilities

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Plot a heatmap of transition probabilities for a multiHMM model.

Usage

heatmapTransitionProbs(
  model = NULL,
  reorder.states = TRUE,
  transitionProbs = NULL
)

Arguments

model	A multiHMM object or file that contains such an object.
reorder.states	Whether or not to reorder the states.
transitionProbs	A matrix with transition probabilities where dimnames(emissionProbs) gives the state labels. This option is helpful to plot transition probabilities directly without needing a chromstaR-objects. If specified, model will be ignored.

Value

A ggplot object.

See Also

plotting

Examples

## Get an example multiHMM ##
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
model <- get(load(file))
## Plot transition probabilites as heatmap
heatmapTransitionProbs(model, reorder.states=TRUE)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.