PlotStates: PlotStates - plotting the results of PaintStates

In Simon-Coetzee/footprintR: StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub

Description

PlotStates - plotting the results of PaintStates

Usage

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

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.