corncob (version 0.4.2)

plot.bbdml: Plotting function

Description

Plotting function

Usage

# S3 method for bbdml
plot(
  x,
  total = FALSE,
  color = NULL,
  shape = NULL,
  facet = NULL,
  title = NULL,
  B = 1000,
  sample_names = TRUE,
  data_only = FALSE,
  ...
)

Value

Object of class ggplot. Plot of bbdml model fit with 95

Arguments

x

Object of class bbdml.

total

(Optional). Default FALSE. Boolean indicator for whether to plot on total counts scale

color

(Optional). Default NULL. The sample variable to map to different colors. Can be a single character string of the variable name in sample_data or a custom supplied vector with length equal to the number of samples. Use a character vector to have ggplot2 default.

shape

(Optional). Default NULL. The sample variable to map to different shapes. Can be a single character string of the variable name in sample_data or a custom supplied vector with length equal to the number of samples.

facet

(Optional). Default NULL. The sample variable to map to different panels in a facet grid. Must be a single character string of a variable name in sample_data.

title

(Optional). Default NULL. Character string. The main title for the graphic.

B

(Optional). Default 1000. Integer. Number of bootstrap simulations for prediction intervals. Use B = 0 for no prediction intervals.

sample_names

(Optional). Default TRUE. Boolean. If FALSE, remove sample names from the plot.

data_only

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

...

There are no optional parameters at this time.

Examples

data(soil_phylum_small_otu1)
mod <- bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)
# Here we use B = 50 for quick demonstration purposes.
# In practice, we recommend a higher value for B for more accurate intervals
plot(mod, color = "DayAmdmt", B = 50)