PlotStates: PlotStates - plotting the results of PaintStates

Description Usage Arguments Value Examples

Description

PlotStates - plotting the results of PaintStates

Usage

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PlotStates(states, location = NULL, gene.track = NULL,
  additional.tracks = NULL)

Arguments

states

A GRangesList produced by PaintStates or a list of GRanges, or GRangesList that has a "score" column, and optionally a "state" column, that is filtered on if the state.select argument is used

location

A GRanges object of length 1, or a character vector of the form: "chr:start-end", e.g., "chr12:51267156-52080611"

gene.track

optionally, an object created by BiomartGeneRegionTrack() to plot the gene context in addition to segmentation.

additional.tracks

optionally, an object of class "AnnotationTrack" with additional data to plot in addition to segmentation.

Value

Plots the states, of the samples in the states object, and if possible the genes in the region

Examples

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load(system.file("extdata", "heart.states.rda", package = "StatePaintR"))
load(system.file("extdata", "vista.heart.enhancers.rda", package = "StatePaintR"))
mylocation <- GRanges("chr1:42623508-42754885")
vista.in.range <- subsetByOverlaps(heart.enhancers, mylocation)
vista.anno <- AnnotationTrack(range = vista.in.range,
                              fill = mcols(vista.in.range)$validated + 2,
                              stacking = "dense",
                              col = NULL,
                              col.line = NULL,
                              stackHeight = 1,
                              shape = "box",
                              rotation.title = 360,
                              background.title = "transparent", col.title = "black",
                              cex.title = 0.5,
                              name = "VISTA enhancers")
PlotStates(states = heart.states,
           location = mylocation,
           additional.tracks = vista.anno)

Simon-Coetzee/footprintR documentation built on May 9, 2019, 1:31 p.m.