TCGAvisualize_meanMethylation {TCGAbiolinks} | R Documentation |
Creates a mean methylation boxplot for groups (groupCol), subgroups will be highlighted as shapes if the subgroupCol was set.
Observation: Data is a summarizedExperiment.
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 )
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 |
Save the pdf survival plot
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")