equalize_ccdb {CellaRepertorium} | R Documentation |
x
The cells in cell_tbl
, and clusters in cluster_tbl
can potentially be a superset of the contig_tbl
.
equalize_ccdb(x, cell = TRUE, contig = TRUE, cluster = TRUE, sort = FALSE)
x |
|
cell |
|
contig |
|
cluster |
|
sort |
|
equalize_ccdb(x, cell = TRUE)
trims cells that aren't in contig_tbl
or cluster_tbl
.
equalize_ccdb(x, cluster = TRUE)
trims clusters that aren't in contig_tbl
.
equalize_ccdb(x, contig = TRUE)
trims contigs that aren't cell_tbl
or cluster_tbl
.
Modification to contig_tbl
(with $
) always equalizes contigs and clusters.
Modification to cell_tbl
equalizes only contigs.
Modification to cluster_tbl
equalizes contigs and clusters.
library(dplyr) tbl = tibble(clust_idx = gl(3, 2), cell_idx = rep(1:3, times = 2), contig_idx = 1:6) ccdb = ContigCellDB(tbl, contig_pk = c('cell_idx', 'contig_idx'), cell_pk = 'cell_idx', cluster_pk = 'clust_idx') # 3 cells ccdb ccdb$cell_tbl = bind_rows(ccdb$cell_tbl, tibble(cell_idx = 0)) # 4 cells now ccdb # 3 cells again equalize_ccdb(ccdb) # remove all contigs from cell 1, and one contig from cell 2 ccdb$contig_tbl = ccdb$contig_tbl[-c(1, 2, 4),] # no changes to cell_tbl yet ccdb # trim cell_tbl to 2 cells, keep all clusters equalize_ccdb(ccdb, cluster = FALSE) # trim both cells and clusters equalize_ccdb(ccdb, cluster = TRUE)