bar and dot plot of effect size of microbiomeMarker data

Source: R/plot-effect-size.R

bar and dot plot of effect size microbiomeMarker data. This function returns a ggplot2 object that can be saved or further customized using ggplot2 package.

plot_ef_bar(mm, label_level = 1, max_label_len = 60, markers = NULL)

plot_ef_dot(mm, label_level = 1, max_label_len = 60, markers = NULL)

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.

Value

a ggplot project

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_ef_bar(mm)