chorddiagram.R

library("circlize")
library("glue")

# Phylum or species/genus
rank <- "phylum"

# Set in and out file names
dffile <- glue("/Users/christopherhempel/Google Drive/PhD UoG/ExStream project/data_files_for_ml/overlap_df_{rank}.csv")
outfile <- glue("/Users/christopherhempel/Google Drive/PhD UoG/ExStream project/exstream_data_visualization_outdir/chorddiagram_{rank}.svg")

# Read in file
## Note: sort df manually before loading it in so that self-connections always come first
df <- read.csv(dffile)

# Set colors
grid.col <- c(
  "ITS-2 ESV" = "#aaa1ff", "ITS-2 OTU" = "#2e7500", "16S ESV" = "#002a90",
  "16S OTU" = "#88e8a6", "Metagenomics" = "#a9006b", "Total RNA-Seq" = "#d4631c"
)

# Set Chord diagram gap options
circos.par(gap.after = c(rep(10, 6)))

# Open the graphics device
svg(outfile, width = 3, height = 3)

# Make Chord diagram
chordDiagram(df,
  grid.col = grid.col, self.link = 1, link.sort = "asis",
  order = c("Metagenomics", "Total RNA-Seq", "ITS-2 OTU", "ITS-2 ESV", "16S ESV", "16S OTU"), annotationTrack = c("grid"), annotationTrackHeight = mm_h(5)
)

for (si in get.all.sector.index()) {
  xlim <- get.cell.meta.data("xlim", sector.index = si, track.index = 1)
  ylim <- get.cell.meta.data("ylim", sector.index = si, track.index = 1)
  circos.text(mean(xlim), mean(ylim), si,
    sector.index = si, track.index = 1,
    facing = "bending.inside", niceFacing = TRUE, col = "white"
  )
}

# Close the graphics device
dev.off()