Automatically creates directories and adds compression based on file name.
write_biom()
- According to BIOM format specification.write_xlsx()
- Raw data and summary tables in Excel file format. See details.write_fasta()
- Sequences only in fasta format.biom
may also be a named character vector.write_tree()
- Phylogenetic tree only in newick format.biom
may also be a phylo object.write_counts()
,write_metadata()
,write_taxonomy()
- Tab-separated values.
Usage
write_biom(biom, file, format = "json")
write_metadata(biom, file, quote = FALSE, sep = "\t", ...)
write_counts(biom, file, quote = FALSE, sep = "\t", ...)
write_taxonomy(biom, file, quote = FALSE, sep = "\t", ...)
write_fasta(biom, file = NULL)
write_tree(biom, file = NULL)
write_xlsx(biom, file, depth = "auto", n = NULL, seed = 0, unc = "singly")
Arguments
- biom
An rbiom object, such as from
as_rbiom()
. Any value accepted byas_rbiom()
can also be given here.- file
Path to the output file. File names ending in
.gz
or.bz2
will be compressed accordingly.write_fasta()
andwrite_tree()
can havefile=NULL
, which returns a string of the output which would have been written.- format
Options are
"tab"
,"json"
, and"hdf5"
, corresponding to classic tabular format, BIOM format version 1.0 and biom version 2.1, respectively. NOTE: to write HDF5 formatted BIOM files, the BioConductor R packagerhdf5
must be installed. Default:"json"
- quote, sep, ...
Parameters passed on to
write.table()
. Default:quote=FALSE, sep="\t"
- depth, n, seed
Passed on to
rarefy_cols()
. Forwrite_xlsx()
only,depth=0
disables rarefaction. Default:depth='auto', n=NULL, seed=0
- seed
Random seed to use in rarefying. See
rarefy_cols()
function for details. Default:0
- unc
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
"singly"
- Replaces them with the OTU name."grouped"
- Replaces them with a higher rank's name."drop"
- Excludes them from the result."asis"
- To not check/modify any taxa names.
Default:
"singly"
Abbreviations are allowed.
Details
For write_xlsx()
, attributes(biom)
are saved as additional worksheets if
the attribute is a data frame, matrix, or dist -class object. An attribute
named 'Reads Per Step' is treated specially and merged with the usual 'Reads
Per Sample' tab.
Examples
library(rbiom)
write_tree(hmp50) %>% substr(1, 50)
#> [1] "(((((((((((((EschC738:0.03627,(((Unc92490:0.05748,"
if (FALSE) {
hmp10 <- hmp50$clone()
hmp10$counts <- hmp10$counts[,1:10] %>% rarefy_cols()
attr(hmp10, "Weighted UniFrac") <- bdiv_distmat(hmp10, 'unifrac')
attr(hmp10, "Unweighted Jaccard") <- bdiv_distmat(hmp10, 'jaccard', weighted=F)
outfile <- write_xlsx(hmp10, tempfile(fileext = ".xlsx"))
}