plot_landscape {microbiome}R Documentation

Landscape Plot

Description

Plot abundance landscape ie. sample density in 2D projection landscape

Usage

plot_landscape(x, method = "NMDS", distance = "bray", col = NULL,
  main = NULL, x.ticks = 10, rounding = 0, add.points = TRUE,
  adjust = 1, size = 1, legend = FALSE)

Arguments

x

phyloseq-class object or a data matrix (features x samples; eg. HITChip taxa vs. samples)

method

Ordination method, see phyloseq::plot_ordination

distance

Ordination distance, see phyloseq::plot_ordination

col

Variable name to highlight samples (points) with colors

main

title text

x.ticks

Number of ticks on the X axis

rounding

Rounding for X axis tick values

add.points

Plot the data points as well

adjust

Kernel width adjustment

size

point size

legend

plot legend TRUE/FALSE

Details

For consistent results, set random seet (set.seed) before function call

Value

A ggplot plot object.

Examples

data(dietswap)
p <- plot_landscape(abundances(transform(dietswap, "log10"))[, 1:2])

[Package microbiome version 1.0.2 Index]