plotClusters: Plot Scores of Cluster Regions

In markrobinsonuzh/Repitools: Epigenomic tools

Plot Scores of Cluster Regions

Description

Given an annotation of gene positions that has a score column, the function will make a series of bar chart plots, one for each cluster.

Usage

  ## S4 method for signature 'data.frame'
plotClusters(x, s.col = NULL, non.cl = NULL, ...)
  ## S4 method for signature 'GRanges'
plotClusters(x, s.col = NULL, non.cl = NULL, ...)

Arguments

x	A summary of genes and their statistical score, and the cluster that they belong to. Either a data.frame or a GRanges. If a data.frame, then (at least) columns chr, start, end, strand, name and cluster. Also a score column, with the column name describing what type of score it is. If a GRanges, then the elementMetadata should have a DataFrame with a score column, and columns named "cluster" and "name".
s.col	The column number of the data.frame when data is a data.frame, or the column number of the DataFrame when data is a GRanges object. The name of this column is used as the y-axis label in the plot.
non.cl	The value in the cluster column that represents genes that are not in any cluster
...	Further parameters to be passed onto plot.

Value

A plot for each cluster is made. Therefore, the PDF device should be opened before this function is called.

Author(s)

Dario Strbenac

Examples

  library(GenomicRanges)
  g.summary <- GRanges("chr1",
                       IRanges(seq(1000, 10000, 1000), width = 100),
                       rep(c('+', '-'), 5),
                       `t-statistic` = rnorm(10, 8, 2),
                       cluster = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 0),
                       name = paste("Gene", 1:10))
  plotClusters(g.summary, 1, 0, ylim = c(4, 12), lwd = 5)

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.