effect_size-plot: bar and dot plot of effect size of microbiomeMarker data

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

bar and dot plot of effect size of microbiomeMarker data

Description

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.

Usage

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)

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