circos

R Markdown

Circos, is a circular ideogram layout to display relationships between genomic intervals.

library("RCircos")
data("UCSC.HG38.Human.CytoBandIdeogram")
cyto.info = UCSC.HG38.Human.CytoBandIdeogram
RCircos.Set.Core.Components(cyto.info, 
                            chr.exclude=NULL, 
                            tracks.inside=10, 
                            tracks.outside=0)

## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

Customising the outer band

Removing the band and stain information from the circos plot and customise the band colors.

cyto.info = UCSC.HG38.Human.CytoBandIdeogram
cyto.info$Name = NA
cyto.info$Stain = NA
RCircos.Set.Core.Components(cyto.info, 
                            chr.exclude=NULL, 
                            tracks.inside=10, 
                            tracks.outside=0)

## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

chr_order = unique(cyto.info$Chromosome)

RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

ideo = RCircos.Get.Plot.Ideogram()
ideo$BandColor = 'salmon'
num = which(ideo$Chromosome == 'chrX')
ideo[num, 'BandColor'] = 'chartreuse'

num = which(ideo$Chromosome == 'chrY')
ideo[num, 'BandColor'] = 'purple'


RCircos.Reset.Plot.Ideogram(ideo)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

num = which(ideo$Chromosome == 'chr1')
ideo[num, 'ChrColor'] = 'goldenrod2'

RCircos.Reset.Plot.Ideogram(ideo)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()


library(biomaRt)

mat = read.csv('/media/user/disk2/completeAnalysis/scRNA_25Aug/RCC1/TC/tumorvsnontumorDEG.csv', row.names = 1)

m = useMart('ensembl', dataset='hsapiens_gene_ensembl')

coords = getBM(attributes=c('chromosome_name', 'start_position', 
                            'end_position', 'hgnc_symbol'),
      filters = c('hgnc_symbol'),
      values = list(rownames(mat)),
      mart = m)

write.csv(coords, file = 'coords.csv')
coords$chromosome_name = paste0('chr', coords$chromosome_name)
coords$chromosome_name = factor(coords$chromosome_name, levels = chr_order)

num = which(is.na(coords$chromosome_name))
coords = coords[-num, ]

up = which((mat$pval < 0.01) &
             (mat$log2FC > 1))
upmat = mat[up, ]

num = which(coords$hgnc_symbol %in% rownames(upmat))
coords1 = coords[num, ]

RCircos.Gene.Name.Plot(coords1, name.col=4, track.num = 2, side = "in",
                       is.sorted = F)

## Not all labels will be plotted.

## Type RCircos.Get.Gene.Name.Plot.Parameters()

## to see the number of labels for each chromosome.

genes = intersect(rownames(mat), coords$hgnc_symbol)

mat1 = mat[genes, ]
df = cbind.data.frame(rownames(mat1), mat1[, c(1,2,4)])
colnames(df)[1] = 'hgnc_symbol'

data = merge(coords, df, by = 'hgnc_symbol', all.x = T)

data = data[, c('chromosome_name', 'start_position',
                'end_position', 'hgnc_symbol',
                'tumor', 'nonTumor', 'log2FC')]
RCircos.Heatmap.Plot(data, data.col = 7, track.num = 6, side = "in",
                     min.value = -3, max.value = 6, 
                    is.sorted = F)

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

RC.param = RCircos.Get.Plot.Parameters()
RC.param['heatmap.color'] = "GreenWhiteRed"
RCircos.Reset.Plot.Parameters(RC.param)

RCircos.Heatmap.Plot(data, data.col = 7, track.num = 10, side = "in",
                     min.value = -2, max.value = 2,
                     is.sorted = F)

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

## Warning in min(theLevel): no non-missing arguments to min; returning Inf

Subsetted circos plots

## 
## RCircos.Core.Components initialized.
## Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

circos

Pranali

2022-10-07

R Markdown

Customising the outer band

Subsetted circos plots