plot the abundances of markers — plot_abundance • microbiomeMarker

plot the abundances of markers

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")