TCGAvisualize_meanMethylation: Mean methylation boxplot

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Mean methylation boxplot

Description

Creates a mean methylation boxplot for groups (groupCol), subgroups will be highlighted 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, median.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")

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.