write_biom | R Documentation |
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.
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 = 0.1, n = NULL, seed = 0, unc = "singly")
biom |
An rbiom object, such as from |
file |
Path to the output file. File names ending in |
format |
Options are |
quote , sep , ... |
Parameters passed on to |
depth , n |
Passed on to |
seed |
Random seed to use in rarefying. See |
unc |
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
Abbreviations are allowed. Default: |
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.
The normalized filepath that was written to (invisibly), unless
file=NULL
(see file
argument above).
library(rbiom)
write_tree(hmp50) %>% substr(1, 50)
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=FALSE)
outfile <- write_xlsx(hmp10, tempfile(fileext = ".xlsx"))
}
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