corncob (version 0.4.2)

plot.differentialTest: differentialTest plot function

Description

differentialTest plot function

Usage

# S3 method for differentialTest
plot(x, level = NULL, data_only = FALSE, ...)

Value

Object of class ggplot. Plot of coefficients from models for significant taxa from differentialTest

Arguments

x

Object of class differentialTest

level

(Optional). Character vector. Desired taxonomic levels for taxa labels.

data_only

(Optional). Default FALSE. Boolean. If TRUE, only returns data frame.

...

No optional arguments are accepted at this time.

Examples

# phyloseq example
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
da_analysis <- differentialTest(formula = ~ DayAmdmt,
                                phi.formula = ~ DayAmdmt,
                                formula_null = ~ 1,
                                phi.formula_null = ~ DayAmdmt,
                                test = "Wald", boot = FALSE,
                                data = soil_phylum_small_otu,
                                sample_data = soil_phylum_small_sample,
                                fdr_cutoff = 0.05,
                                try_only = 1:5)
plot(da_analysis, level = "Phylum")