phyloseq2table: Phyloseq conversion to a ggplot-formatted table

In nyoungb2/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

Convert the OTU table (+ metadata) to a format that can be easily plotted with phyloseq

Usage

phyloseq2table(physeq, include_sample_data = FALSE, sample_col_keep = NULL,
  include_tax_table = FALSE, tax_col_keep = NULL, control_expr = NULL)

Arguments

physeq	Phyloseq object
include_sample_data	Include sample_table information?
sample_col_keep	Which columns in the sample_data table to keep? Use NULL to keep all columns.
include_tax_table	Include tax_table information?
tax_col_keep	A vector for column names to keep. Use NULL to keep all columns.
control_expr	An expression for identifying which samples are controls. Control/non-control identification will be in the 'IS_CONTROL' column of the returned data.frame object.

Value

data.frame

Examples

data(physeq_S2D1)
# Including some columns from sample metadata
df_OTU = phyloseq2table(physeq_S2D1,
                        include_sample_data=TRUE,
                        sample_col_keep=c('Buoyant_density', 'Substrate', 'Day'))
head(df_OTU)

## Not run: 
# Including some columns from sample metadata & taxonomy
df_OTU = phyloseq2table(physeq_S2D1,
                        include_sample_data=TRUE,
                        sample_col_keep=c('Buoyant_density', 'Substrate', 'Day'),
                        include_tax_table=TRUE)
head(df_OTU)

## End(Not run)

nyoungb2/HTSSIP documentation built on May 24, 2019, 11:51 a.m.