examples/circosPlot-examples.R

In mixOmicsTeam/mixOmics: Omics Data Integration Project

data(nutrimouse)
Y = nutrimouse$diet
data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid)
design = matrix(c(0,1,1,1,0,1,1,1,0), ncol = 3, nrow = 3, byrow = TRUE)


nutrimouse.sgccda <- wrapper.sgccda(X=data,
Y = Y,
design = design,
keepX = list(gene=c(10,10), lipid=c(15,15)),
ncomp = 2,
scheme = "horst")

circosPlot(nutrimouse.sgccda, cutoff = 0.7)
## links widths based on strength of their similarity
circosPlot(nutrimouse.sgccda, cutoff = 0.7, linkWidth = c(1, 10))
## custom legend
circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1)

## more customisation
circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1, color.Y = 1:5, 
           color.blocks = c("green","brown"), color.cor = c("magenta", "purple"))
    
par(mfrow=c(2,2))

circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1)
## also show intra-block correlations
circosPlot(nutrimouse.sgccda, cutoff = 0.7,
           size.legend = 1.1, showIntraLinks = TRUE)
## show lines
circosPlot(nutrimouse.sgccda, cutoff = 0.7, line = TRUE, ncol.legend = 1,
           size.legend = 1.1, showIntraLinks = TRUE)
## custom line legends
circosPlot(nutrimouse.sgccda, cutoff = 0.7, line = TRUE, ncol.legend = 2,
           size.legend = 1.1, showIntraLinks = TRUE)
par(mfrow=c(1,1))

## adjust feature and block names radially
circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1)
circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1, 
           var.adj = 0.8, block.labels.adj = -0.5)
## ---  example using breast.TCGA data
data("breast.TCGA")
data = list(mrna = breast.TCGA$data.train$mrna, 
            mirna = breast.TCGA$data.train$mirna, 
            protein = breast.TCGA$data.train$protein)
list.keepX = list(mrna = rep(20, 2), mirna = rep(10,2), protein = c(10, 2))

TCGA.block.splsda = block.splsda(X = data, 
                             Y =breast.TCGA$data.train$subtype,
                             ncomp = 2, keepX = list.keepX, 
                             design = 'full')
circosPlot(TCGA.block.splsda, cutoff = 0.7, line=TRUE)
## show only first 2 blocks
circosPlot(TCGA.block.splsda, cutoff = 0.7, line=TRUE, blocks = c(1,2))
## show only correlations including the mrna block features
circosPlot(TCGA.block.splsda, cutoff = 0.7, blocks.link = 'mrna')

data("breast.TCGA")
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna)
list.keepX = list(mrna = rep(20, 2), mirna = rep(10,2))
list.keepY = c(rep(10, 2))

TCGA.block.spls = block.spls(X = data, 
                             Y = breast.TCGA$data.train$protein,
                             ncomp = 2, keepX = list.keepX, 
                             keepY = list.keepY, design = 'full')
circosPlot(TCGA.block.spls, group = breast.TCGA$data.train$subtype, cutoff = 0.7, 
           Y.name = 'protein')
## only show links including mrna
circosPlot(TCGA.block.spls, group = breast.TCGA$data.train$subtype, cutoff = 0.7, 
           Y.name = 'protein', blocks.link = 'mrna')