TCGAbiolinks (version 1.2.5)

TCGAvisualize_meanMethylation: 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 = FALSE, 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()}