phyloseq2table {HTSSIP} | R Documentation |
Phyloseq conversion to a ggplot-formatted table
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_col_keep |
Which columns in the |
include_tax_table |
Include |
tax_col_keep |
A vector for column names to keep.
Use |
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)
[Package HTSSIP version 1.4.1 Index]