plot_spaghetti: Spaghetti Plots

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Spaghetti Plots

Description

Spaghetti Plots

Usage

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

## Not run: 
# 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)

## End(Not run)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.