Spaghetti Plots — plot_spaghetti • microbiomeutilities

Spaghetti Plots

plot_spaghetti(
  x,
  plot.var = "by_taxa",
  select.taxa = NULL,
  xvar = NULL,
  group = NULL,
  line.bg.color = "#8d99ae",
  bg.opacity = 0.5,
  focus.color = "brown3",
  ncol = NULL,
  nrow = NULL,
  focus.line.size = 0.5,
  line.size = 1
)

Arguments

x: phyloseq-class object
plot.var: One of "by_sample":Many sample one taxa or "by_taxa":Many taxa one sample
select.taxa: a character list of taxa to be plotted. eg. select.taxa <- c("OTU-370251", "OTU-311173", "OTU-341024").
xvar: X-axis variable. This can be visit_number for participants in subject_id.
group: Column describing sample that have multiple measurements. For e.g. Subject_Ids which has all subject_ids listed.
line.bg.color: Line color for background. Default ="#8d99ae",
bg.opacity: Line opacity for background.
focus.color: Line color for focus being plotted.
ncol: if wrap, specify number of columns.
nrow: if wrap, specify number of rows.
focus.line.size: Line size for focus being plotted.
line.size: Line size for background.

Value

ggplot object. This can be further modified using ggpubr.

Examples

if (FALSE) {
# Example data
library(microbiomeutilities)
data("hmp2")
pseq <- hmp2 # Ren
pseq.rel <- microbiome::transform(pseq, "compositional")
pseq.relF <- format_to_besthit(pseq.rel)
# Choose one participant
phdf.s <- subset_samples(pseq.relF, subject_id ==
  "Participant_1")
# Choose top 12 taxa to visualize
ntax <- top_taxa(phdf.s, 12)
phdf.s <- prune_taxa(ntax, phdf.s)

plot_spaghetti(phdf.s,
  plot.var = "by_taxa",
  select.taxa = ntax,
  xvar = "visit_number",
  line.bg.color = "#8d99ae",
  focus.color = "#555b6e",
  ncol = 3,
  nrow = 4,
  line.size = 0.2
)

print(p)
}