plot_area: Area plot

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Area plot

Description

Create an area plot for longitudinal samples with ggplot2 package.

Usage

plot_area(
  x,
  xvar = NULL,
  level = NULL,
  facet.by = NULL,
  fill.colors = brewer.pal(6, "Paired"),
  abund.thres = 0.001,
  prev.thres = 0.5,
  ncol = 5,
  nrow = 5
)

Arguments

x	phyloseq-class object.
xvar	Column name to plot on x-axis.
level	Taxonomic level. OTU/ASV level not supported.
facet.by	Column with variable that has multiple measurements.
fill.colors	brewer.pal(6,"Paired"). Specify colors.
abund.thres	= 0.001 check microbiome package aggregate_rare function.
prev.thres	= 0.1 check microbiome package aggregate_rare function.
ncol	wrap, specify number of columns.
nrow	wrap, specify number of rows.

Value

ggplot object.

Examples

## Not run: 
library(microbiomeutilities)
data("hmp2")
ps <- hmp2
ps.rel <- microbiome::transform(ps, "compositional") 
p <- plot_area(ps.rel, xvar="visit_number", 
              level = "Phylum",
              facet.by = "subject_id",
              fill.colors=brewer.pal(6,"Paired"))

## End(Not run)           

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