prop_tax_row: Propagate taxon information in a single row of a 'tax_table'...
In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data
View source: R/prop_tax_down.R
prop_tax_row R Documentation
Propagate taxon information in a single row of a tax_table object.
Description
prop_tax_row Takes the taxon assignment from the lowest assigned level
in an OTU's assignment and fills it in to all the lower, unresolved fields.
Usage
prop_tax_row(taxrow, indic)
Arguments
taxrow
A single row in a taxon table
indic
a flag to indicate if the taxon names have level indicators.
If FALSE, they are added.
Details
Often taxon cannot be assigned all the way down to genus
from the limited information available from a given variable region of 16S
(or other marker gene). If an OTU has been assigned to Order
Enterobacteriales, but the Family and genus cannot be resolved, then the
Family and Genus fields are left blank by QIIME. This function fills those
fields with the string 'o_Enterobacteriales', so they are not parsed as NAs
by ggplot and other functions.
Value
A single row tax_table object to with NAs replaced
with higher-level taxon assignments
JCSzamosi/aftersl1p documentation built on July 3, 2025, 8:37 p.m.
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View source: R/prop_tax_down.R
| prop_tax_row | R Documentation |
Propagate taxon information in a single row of a tax_table object.
Description
prop_tax_row Takes the taxon assignment from the lowest assigned level
in an OTU's assignment and fills it in to all the lower, unresolved fields.
Usage
prop_tax_row(taxrow, indic)
Arguments
taxrow |
A single row in a taxon table |
indic |
a flag to indicate if the taxon names have level indicators. If FALSE, they are added. |
Details
Often taxon cannot be assigned all the way down to genus from the limited information available from a given variable region of 16S (or other marker gene). If an OTU has been assigned to Order Enterobacteriales, but the Family and genus cannot be resolved, then the Family and Genus fields are left blank by QIIME. This function fills those fields with the string 'o_Enterobacteriales', so they are not parsed as NAs by ggplot and other functions.
Value
A single row tax_table object to with NAs replaced
with higher-level taxon assignments
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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