plot_abundance: plot the abundances of markers

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

plot the abundances of markers

Description

plot the abundances of markers

Usage

plot_abundance(mm, label_level = 1, max_label_len = 60, markers = NULL, group)

Arguments

mm	a microbiomeMarker object
label_level	integer, number of label levels to be displayed, default 1, 0 means display the full name of the feature
max_label_len	integer, maximum number of characters of feature label, default 60
markers	character vector, markers to display, default NULL, indicating plot all markers.
group	character, the variable to set the group

Value

a ggplot2::ggplot object.

Examples

data(enterotypes_arumugam)
mm <- run_limma_voom(
    enterotypes_arumugam,
    "Enterotype",
    contrast = c("Enterotype 3", "Enterotype 2"),
    pvalue_cutoff = 0.01,
    p_adjust = "none"
)
plot_abundance(mm, group = "Enterotype")

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.