Microbiome figure in R

Making figures for microbiome data in RStudio

This is an attempt to collate some useful commonly used figures for microbiome visualization.

Also applicable to data viz more generally.

At the moment I have this information spread across many different places.

🔗 Some links to this include

• Project website for publication on microbiome in wildlife & ticks
• Project website for publication on haemoprotozoa in wildlife & ticks
• 2022 BIO514 workshop
• 2021 BIO514 workshop
• 2021 BIO510 workshop
• Cryptick Lab NGS webpage

Packing circles

R gallery

Using packcircles R package

Static image of packed circle plot

#install.packages("packcircles")
library(packcircles)
data("bacteria")

packing <- circleProgressiveLayout(bacteria)
dat.gg <- circleLayoutVertices(packing)
ggplot(data = dat.gg) +
  geom_polygon(aes(x, y, group = id, fill = factor(id)),
               colour = "black",
               show.legend = FALSE) +
  scale_fill_manual(values = bacteria$colour) +
  scale_y_reverse() +
  coord_equal()

Interactive figure for packed circle taxonomy plot

if (requireNamespace("ggiraph"))
  gg <- ggplot(data = dat.gg) +
    ggiraph::geom_polygon_interactive(
      aes(
        x,
        y,
        group = id,
        fill = factor(id),
        tooltip = bacteria$label[id],
        data_id = id
      ),
      colour = "black",
      show.legend = FALSE
    ) +
    scale_fill_manual(values = bacteria$colour) +
    scale_y_reverse() +
    labs(title = "Hover over circle to display taxon name") +
    coord_equal()

ggiraph::ggiraph(ggobj = gg,
                 width_svg = 5,
                 height_svg = 5)
  

Using circlepackeR R package

See package here jeromefroe/circlepackeR, to install devtools::install_github("jeromefroe/circlepackeR")

library(microbiome)
library(circlepackeR)
library(tidyverse)
library(hrbrthemes)
library(data.tree)
library(htmlwidgets)

s <- aggregate_taxa(ps, 'Genus')
melts <- psmelt(s)
test <- melts
# subset just the collowing column: Kingdom, Class, Order, Family, Genus
test <- test[, c(12, 13, 15, 16, 17, 3)]
test <- subset(test, Abundance > 0)

test$pathString <-
  paste(test$Kingdom,
        test$Phylum,
        test$Class,
        test$Order,
        test$Family,
        test$Genus,
        sep = "/")
nodetest <- as.Node(test)
all <- circlepackeR(nodetest, size = "Abundance")

# save html
saveWidget(all, file = "packedCircle_all.html")
# save pdf
# Make a webshot in pdf : high quality but can not choose printed zone
webshot("packedCircle_all.html" , "packedCircle_all.pdf")
# save png
# Make a webshot in png : Low quality - but you can choose shape
webshot(
  "packedCircle_all.html" ,
  "packedCircle_all.png",
  delay = 0.2 ,
  cliprect = c(440, 0, 1000, 10)
)