TCGAvisualize_meanMethylation {TCGAbiolinks} | R Documentation

## Mean methylation boxplot

### Description

Creates a mean methylation boxplot for groups (groupCol), subgroups will be highlited as shapes if the subgroupCol was set.

Observation: Data is a summarizedExperiment.

### Usage

    TCGAvisualize_meanMethylation(data, groupCol = NULL,
      subgroupCol = NULL, shapes = NULL, print.pvalue = FALSE,
      plot.jitter = TRUE, jitter.size = 3, filename = "groupMeanMet.pdf",
      ylab = expression(paste("Mean DNA methylation (", beta, "-values)")),
      xlab = NULL, title = "Mean DNA methylation", labels = NULL,
      group.legend = NULL, subgroup.legend = NULL, color = NULL,
      y.limits = NULL, sort, order, legend.position = "top",
      legend.title.position = "top", legend.ncols = 3,
      add.axis.x.text = TRUE, width = 10, height = 10, dpi = 600,
      axis.text.x.angle = 90)

### Arguments

`data` | SummarizedExperiment object obtained from TCGAPrepare
`groupCol` | Columns in colData(data) that defines the groups. If no columns defined a columns called "Patients" will be used
`subgroupCol` | Columns in colData(data) that defines the subgroups.
`shapes` | Shape vector of the subgroups. It must have the size of the levels of the subgroups. Example: shapes = c(21,23) if for two levels
`print.pvalue` | Print p-value for two groups
`plot.jitter` | Plot jitter? Default TRUE
`jitter.size` | Plot jitter size? Default 3
`filename` | The name of the pdf that will be saved
`ylab` | y axis text in the plot
`xlab` | x axis text in the plot
`title` | main title in the plot
`labels` | Labels of the groups
`group.legend` | Name of the group legend. DEFAULT: groupCol
`subgroup.legend` | Name of the subgroup legend. DEFAULT: subgroupCol
`color` | vector of colors to be used in graph
`y.limits` | Change lower/upper y-axis limit
`sort` | Sort boxplot by mean or median. Possible values: mean.asc, mean.desc, median.asc, meadian.desc
`order` | Order of the boxplots
`legend.position` | Legend position ("top", "right","left","bottom")
`legend.title.position` | Legend title position ("top", "right","left","bottom")
`legend.ncols` | Number of columns of the legend
`add.axis.x.text` | Add text to x-axis? Default: FALSE
`width` | Plot width default:10
`height` | Plot height default:10
`dpi` | Pdf dpi default:600
`axis.text.x.angle` | Angle of text in the x axis

### Value

Save the pdf survival plot

### Examples

    nrows <- 200; ncols <- 21
    counts <- matrix(runif(nrows * ncols, 0, 1), nrows)
    rowRanges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                       IRanges::IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                        strand=sample(c("+", "-"), 200, TRUE),
                        feature_id=sprintf("ID%03d", 1:200))
    colData <- S4Vectors::DataFrame(Treatment=rep(c("ChIP", "Input","Other"), 7),
                        row.names=LETTERS[1:21],
                        group=rep(c("group1","group2","group3"),c(7,7,7)),
                        subgroup=rep(c("subgroup1","subgroup2","subgroup3"),7))
    data <- SummarizedExperiment::SummarizedExperiment(
             assays=S4Vectors::SimpleList(counts=counts),
             rowRanges=rowRanges,
             colData=colData)
    TCGAvisualize_meanMethylation(data,groupCol  = "group")
    # change lower/upper y-axis limit
    TCGAvisualize_meanMethylation(data,groupCol  = "group", y.limits = c(0,1))
    # change lower y-axis limit
    TCGAvisualize_meanMethylation(data,groupCol  = "group", y.limits = 0)
    TCGAvisualize_meanMethylation(data,groupCol  = "group", subgroupCol="subgroup")
    TCGAvisualize_meanMethylation(data,groupCol  = "group")
    TCGAvisualize_meanMethylation(data,groupCol  = "group",sort="mean.desc",filename="meandesc.pdf")
    TCGAvisualize_meanMethylation(data,groupCol  = "group",sort="mean.asc",filename="meanasc.pdf")
    TCGAvisualize_meanMethylation(data,groupCol  = "group",sort="median.asc",filename="medianasc.pdf")
    TCGAvisualize_meanMethylation(data,groupCol  = "group",sort="median.desc",filename="mediandesc.pdf")
    if (!(is.null(dev.list()["RStudioGD"]))){dev.off()}

[Package TCGAbiolinks version 2.10.5 Index]