circlize

circlize.md

First, a tab-delimited file with genome sizes

Gm01	58711475	26	60	61
Gm03	52519505	59690052	60	61

etc.

Then, to plot the thing:

library(cowplot)
library(circlize)
library(RColorBrewer)
library(tidyverse)

circos.par("track.height" = 0.2)

#### Plot chromosomes
chrom_frame <- read_tsv('genome.list', col_names =
                          c('chr', 'end', 'bla', 'blu', 'bli'))
chrom_frame$start <- 0
chrom_frame <- chrom_frame %>% select(chr, start, end)


genes <- read_delim(
  'new.pansoy.gff',
  '\t',
  col_names = c(
    'Chrom',
    'source',
    'type',
    'start',
    'end',
    'strand',
    'strand2',
    'phase',
    'names'
  )
) %>% filter(type == 'gene')

genes <- genes %>% filter(str_detect(Chrom, 'Gm'))

circos.genomicInitialize(chrom_frame)

mycol <- brewer.pal(5, 'Dark2')

### Plot regular gene density
genes_bed <- genes %>% select('Chrom', 'start', 'end') 
names(genes_bed ) <- c('chr', 'start', 'end')

newgenes_bed <- tibble('chr' = character(),'start' =numeric(), 'end'=numeric())

# some code to flip start and end coordinates around for negative strand genes
for(i in 1:nrow(genes_bed)) {
  this_gene <- genes_bed[i,]
  if (this_gene$start > this_gene$end) {
    temp = this_gene$start
    this_gene$start = this_gene$end
    this_gene$end = temp
  }
  newgenes_bed <- bind_rows(newgenes_bed, this_gene)
}

circos.genomicDensity(as.data.frame(newgenes_bed), col=mycol[1])

At this point we have one track, the gene density. The rest of my code is various gffs etc. getting fed to circos.genomicDensity().

I've also made dotplots, for some reason those need lists of data-frames:

in_up_list <- list(newwild_modern_increase_genes_bed, newwild_modern_decrease_genes_bed)
circos.genomicRainfall(in_up_list, col=c(mycol[3], mycol[4]),pch=16, cex=0.4)

To save with fancier libraries:

p <- recordPlot() # save the current plot
library(cowplot)
save_plot(filename='circos.png', 
          plot=replayPlot(p), 
          base_height=6)