Package 'phylotaR'

Description

Returns a tree with added clade

Usage

addClade(tree, id, clade)

Arguments

Details

Add a TreeMan object to an existing TreeMan object by specifying an ID at which to attach. If the id specified is an internal node, then the original clade descending from that node will be replaced. Before running, ensure no IDs are shared between the tree and the clade, except for the IDs in the clade of that tree that will be replaced. Note, returned tree will not have a node matrix.

See Also

rmClade, getSubtree, https://github.com/DomBennett/treeman/wiki/manip-methods

Examples

t1 <- randTree(100)
# extract a clade
cld <- getSubtree(t1, "n2")
# remove the same clade
t2 <- rmClade(t1, "n2")
# add the clade again
t3 <- addClade(t2, "n2", cld)
# t1 and t3 should be the same
# note there is no need to remove a clade before adding
t3 <- addClade(t1, "n2", cld) # same tree

Description

Return tree with node matrix added.

Usage

addNdmtrx(tree, shared = FALSE, ...)

Arguments

Details

The node matrix makes 'enquiry'-type computations faster: determining node ages, number of descendants etc. But it takes up large amounts of memory and has no impact on adding or removing tips. Note, trees with the node matrix can not be written to disk using the 'serialization format' i.e. with save or saveRDS. The matrix is generated with bigmemory's 'as.big.matrix()'.

See Also

updateSlts, rmNdmtrx, https://cran.r-project.org/package=bigmemory

Examples

#
tree <- randTree(10, wndmtrx = FALSE)
summary(tree)
tree <- addNdmtrx(tree)
summary(tree)

Description

Returns a tree with a new tip ID added

Usage

addTip(
  tree,
  tid,
  sid,
  strt_age = NULL,
  end_age = 0,
  tree_age = NULL,
  pid = paste0("p_", tid)
)

Arguments

Details

User must provide new tip ID, the ID of the node which will become the new tip's sister, and new branch lengths. The tip ID must only contain letters numbers and underscores. Optionally, user can specify the IDs for the new parental internal nodes. Ensure that the strt_age is greater than the end_age, and that the strt_age falls within the age span of the sister ID. Otherwise, negative spns may be produced leading to an error. Note, returned tree will not have a node matrix. Note, providing negative end ages will increase the age of the tree.

See Also

rmTips, https://github.com/DomBennett/treeman/wiki/manip-methods

Examples

tree <- randTree(10)
tree_age <- getAge(tree)
possible_ages <- getSpnAge(tree, "t1", tree_age)
start_age <- runif(1, possible_ages[["end"]], possible_ages[["start"]])
end_age <- possible_ages[["end"]]
tree <- addTip(tree,
  tid = "t11", sid = "t1", strt_age = start_age,
  end_age = end_age, tree_age = tree_age
)
summary(tree)

Description

aotus

Format

A TreeMan or Phylota object

Examples

data("aotus")

Description

Run downloader function in batches for sequences or taxonomic records

Usage

batcher(ids, func, ps, lvl = 0)

Arguments

Value

Vector of records

vector of rentrez function results

See Also

Other run-private: blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

birds

Format

A TreeMan or Phylota object

Examples

data("birds")

Description

Find single-linkage clusters from BLAST results. Identifies seed sequence.

Usage

blast_clstr(blast_res)

Arguments

Value

List of list

list of cluster descriptions

See Also

Other run-private: batcher(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Given a BLAST output, filters query-subject pairs such that only HSPs with a coverage greater than mncvrg (specified in the pipeline parameters) remain. Filters both: query-subject and subject-query pairs, if one of the coverages is insufficient. HSP coverage is obtained from the BLAST column qcovs.

Usage

blast_filter(blast_res, ps, lvl = 3)

Arguments

Value

data.frame blast res

See Also

Other run-private: batcher(), blast_clstr(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Ensures NCBI BLAST executables are installed on the system. Tests version number of BLAST tools.

Usage

blast_setup(d, v, wd, otsdr)

Arguments

Details

BLAST tools must be version >= 2.0

Value

list

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Return BLAST results from BLASTing all vs all for given sequences. Returns NULL if no BLAST results generated.

Usage

blast_sqs(txid, typ, sqs, ps, lvl)

Arguments

Value

blast_res data.frame or NULL

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Run to load cached BLAST results.

Usage

blastcache_load(sids, wd)

Arguments

Value

blast_res data.frame or NULL

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Run whenever local BLAST runs are made to save results in cache in case the pipeline is run again.

Usage

blastcache_save(sids, wd, obj)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Generate BLAST database in wd for given sequences.

Usage

blastdb_gen(sqs, dbfl, ps)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Use blastn to BLAST all-vs-all using a BLAST database.

Usage

blastn_run(dbfl, outfl, ps)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Returns a balanced TreeMan tree with n tips.

Usage

blncdTree(n, wndmtrx = FALSE, parallel = FALSE)

Arguments

Details

Equivalent to ape's stree(type='balanced') but returns a TreeMan tree. Tree is always rooted and bifurcating.

See Also

TreeMan-class, randTree, unblncdTree

Examples

tree <- blncdTree(5)

Description

bromeliads

Format

A TreeMan or Phylota object

Examples

data("bromeliads")

Description

Deletes a cache from a wd.

Usage

cache_rm(wd)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Creates a cache of parameters in the wd.

Usage

cache_setup(ps, ovrwrt = FALSE)

Arguments

Details

Warning: overwriting with this function will delete the existing cache.

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

For all sequences in a cluster(s) the MAD score.

Usage

calc_mad(phylota, cid)

Arguments

Details

MAD is a measure of the deviation in sequence length of a cluster. Values range from 0 to 1. Clusters with values close to 1 have sequences with similar lengths.

Value

vector

See Also

Other tools-public: calc_wrdfrq(), drop_by_rank(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota(), write_sqs()

Examples

data("bromeliads")
random_cids <- sample(bromeliads@cids, 10)
(calc_mad(phylota = bromeliads, cid = random_cids))

Description

For all sequences in a cluster(s) calculate the frequency of separate words in either the sequence definitions or the reported feature name.

Usage

calc_wrdfrq(
  phylota,
  cid,
  min_frq = 0.1,
  min_nchar = 1,
  type = c("dfln", "nm"),
  ignr_pttrn = "[^a-z0-9]"
)

Arguments

Details

By default, anything that is not alphanumeric is ignored. 'dfln' and 'nm' match the slot names in a SeqRec, see list_seqrec_slots().

Value

list

See Also

Other tools-public: calc_mad(), drop_by_rank(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota(), write_sqs()

Examples

data('dragonflies')
# work out what gene region the cluster is likely representing with word freqs.
random_cids <- sample(dragonflies@cids, 10)
# most frequent words in definition line
(calc_wrdfrq(phylota = dragonflies, cid = random_cids, type = 'dfln'))
# most frequent words in feature name
(calc_wrdfrq(phylota = dragonflies, cid = random_cids, type = 'nm'))

Description

Returns the branch length distance between two trees.

Usage

calcDstBLD(tree_1, tree_2, nrmlsd = FALSE, parallel = FALSE, progress = "none")

Arguments

Details

BLD is the Robinson-Foulds distance weighted by branch length. Instead of summing the differences in partitions between the two trees, the metric takes the square root of the squared difference in branch lengths. Parallelizable.

References

Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11, 459-468.

See Also

calcDstTrp, calcDstRF https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree_1 <- randTree(10)
tree_2 <- randTree(10)
calcDstBLD(tree_1, tree_2)

Description

Returns a distance matrix for specified ids of a tree.

Usage

calcDstMtrx(tree, ids, parallel = FALSE, progress = "none")

Arguments

Details

The distance between every id in the tree is calculated by summing the lengths of the branches that connect them. This can be useful for testing the distances between trees, checking for evoltuionary isolated tips etc. Parallelizable.

See Also

calcDstBLD, calcDstRF, calcDstTrp https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

# checking the distance between two trees

tree_1 <- randTree(10)
tree_2 <- randTree(10)
dmat1 <- calcDstMtrx(tree_1, tree_1["tips"])
dmat2 <- calcDstMtrx(tree_2, tree_2["tips"])
mdl <- cor.test(x = dmat1, y = dmat2)
as.numeric(1 - mdl$estimate) # 1 - Pearson's r

Description

Returns the Robinson-Foulds distance between two trees.

Usage

calcDstRF(tree_1, tree_2, nrmlsd = FALSE)

Arguments

Details

RF distance is calculated as the sum of partitions in one tree that are not shared by the other. The maximum number of split differences is the total number of nodes in both trees (excluding the roots). Trees are assumed to be bifurcating, this is not tested. The metric is calculated as if trees are unrooted. Parallelizable.

References

Robinson, D. R.; Foulds, L. R. (1981). "Comparison of phylogenetic trees". Mathematical Biosciences 53: 131-147.

See Also

calcDstBLD, calcDstTrp https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree_1 <- randTree(10)
tree_2 <- randTree(10)
calcDstRF(tree_1, tree_2)

Description

Returns the triplet distance between two trees.

Usage

calcDstTrp(tree_1, tree_2, nrmlsd = FALSE, parallel = FALSE, progress = "none")

Arguments

Details

The triplet distance is calculated as the sum of different outgroups among every triplet of tips between the two trees. Normalisation is performed by dividing the resulting number by the total number of triplets shared between the two trees. The triplet distance is calculated only for shared tips between the two trees. Parallelizable.

References

Critchlow DE, Pearl DK, Qian C. (1996) The Triples Distance for rooted bifurcating phylogenetic trees. Systematic Biology, 45, 323-34.

See Also

calcDstBLD, calcDstRF https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree_1 <- randTree(10)
tree_2 <- randTree(10)
calcDstTrp(tree_1, tree_2)

Description

Returns the evolutationary distinctness of ids using the fair proportion metric.

Usage

calcFrPrp(tree, tids, progress = "none")

Arguments

Details

The fair proportion metric calculates the evolutionary distinctness of tips in a tree through summing the total amount of branch length each tip represents, where each branch in the tree is evenly divided between all descendants. Parallelizable.

References

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.

See Also

calcPhyDv, calcPrtFrPrp, https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcFrPrp(tree, tree["tips"])

Description

Returns the balance of a node.

Usage

calcNdBlnc(tree, id)

Arguments

Details

Balance is calculated as the absolute difference between the number of descendents of the two bifurcating edges of a node and the expected value for a balanced tree. NA is returned if the node is polytomous or a tip.

See Also

calcNdsBlnc, https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcNdBlnc(tree, id = tree["root"]) # root balance

Description

Returns the absolute differences in number of descendants for bifurcating branches of every node

Usage

calcNdsBlnc(tree, ids, parallel = FALSE, progress = "none")

Arguments

Details

Runs calcNdBlnc() across all node IDs. NA is returned if the node is polytomous. Parallelizable.

See Also

calcNdBlnc, https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcNdsBlnc(tree, ids = tree["nds"])

Description

Returns the sum of branch lengths represented by ids_1 and ids_2 for a tree.

Usage

calcOvrlp(
  tree,
  ids_1,
  ids_2,
  nrmlsd = FALSE,
  parallel = FALSE,
  progress = "none"
)

Arguments

Details

Use this to calculate the sum of branch lengths that are represented between two communities. This measure is also known as the unique fraction. It can be used to measure concepts of phylogenetic turnover. Parallelizable.

References

Lozupone, C., & Knight, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71(12), 8228-35.

See Also

calcPhyDv https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
ids_1 <- sample(tree["tips"], 5)
ids_2 <- sample(tree["tips"], 5)
calcOvrlp(tree, ids_1, ids_2)

Description

Returns the phylogenetic diversity of a tree for the tips specified.

Usage

calcPhyDv(tree, tids, parallel = FALSE, progress = "none")

Arguments

Details

Faith's phylogenetic diversity is calculated as the sum of all connected branches for specified tips in a tree. It can be used to investigate how biodviersity as measured by the phylogeny changes. Parallelizable. The function uses getCnntdNds().

References

Faith, D. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

See Also

calcFrPrp, calcOvrlp, getCnnctdNds, https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcPhyDv(tree, tree["tips"])

Description

Returns the evolutationary distinctness of ids using the fair proportion metric.

Usage

calcPrtFrPrp(tree, tids, ignr = NULL, progress = "none")

Arguments

Details

Extension of calcFrPrp() but with ignore argument. Use ignr to ignore certain tips from calculation. For example, if any of tips are extinct you may wish to ignore these.

References

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.

See Also

calcFrPrp https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

tree <- randTree(10)
calcPrtFrPrp(tree, c("t1", "t3"), ignr = "t2")

Description

Return T/F fpr ndlst consistency

Usage

checkNdlst(ndlst, root)

Arguments

Details

Tests whether each node in tree points to valid other node IDs. Also ensures 'spn' and 'root' are correct. Reports nodes that have errors.

See Also

fastCheckTreeMan, checkTreeMen

Examples

tree <- randTree(100)
(checkNdlst(tree@ndlst, tree@root))

Description

Return T/F if trees is a true TreeMen object

Usage

checkTreeMen(object)

Arguments

Details

Tests whether all trees in object are TreeMan objects

See Also

checkNdlst

Description

All nodes with less than maximum number of nodes and sequences.

Usage

clade_select(txdct, ps)

Arguments

Value

vector of txids

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Identifies all direct and subtree clusters for a taxonomic ID.

Usage

clstr_all(txid, sqs, txdct, ps, lvl = 0)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

In GenBank certain sequences may only be associated with a higher level taxon (e.g. genus, family ...). This function generates clusters from these sequences, alone. This function identifies such sequences in the sequence object and generates a list of clusters of cl_type 'direct'.

Usage

clstr_direct(txid, sqs, txdct, ps, lvl)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Given a sequence object, this function will generate a list of cluster objects using BLAST

Usage

clstr_sqs(txid, sqs, ps, lvl, typ = c("direct", "subtree", "paraphyly"))

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Identifies clusters from sequences associated with a txid and all its descendants. Clusters returned by this function will thus be of cl_type 'subtree'.

Usage

clstr_subtree(txid, sqs, txdct, dds, ps, lvl)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Loads cluster sets from cache. Extracts seed sequences and runs all-v-all BLAST of seeds to identify sister clusters. Sisters are then merged. An object of all sequences and clusters is then saved in cache.

Usage

clstr2_calc(ps)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Takes a list of ClstrRecs, returns a ClstrArc.

Usage

clstrarc_gen(clstrrecs)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Take two ClstrArc classes and join them into a single ClstrArc.

Usage

clstrarc_join(clstrarc_1, clstrarc_2)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Multiple cluster records.

Usage

## S4 method for signature 'ClstrArc'
as.character(x)

## S4 method for signature 'ClstrArc'
show(object)

## S4 method for signature 'ClstrArc'
print(x)

## S4 method for signature 'ClstrArc'
str(object, max.level = 2L, ...)

## S4 method for signature 'ClstrArc'
summary(object)

## S4 method for signature 'ClstrArc,character'
x[[i]]

## S4 method for signature 'ClstrArc,character,missing,missing'
x[i, j, ..., drop = TRUE]

Arguments

Slots

ids

Vector of cluster record IDs

clstrs

List of ClstrArc named by ID

See Also

Other run-public: ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

data('aotus')
clstrarc <- aotus@clstrs
# this is a ClstrArc object
# it contains cluster records
show(clstrarc)
# you can access its different data slots with @
clstrarc@ids     # unique cluster ID
clstrarc@clstrs  # list of cluster records
# access cluster records [[
(clstrarc[[clstrarc@ids[[1]]]])  # first cluster record
# generate new cluster archives with [
(clstrarc[clstrarc@ids[1:10]])  # first 10 clusters

Description

Takes a list of lists of cluster descriptions and generates ClstrRecs.

Usage

clstrrec_gen(clstr_list, txid, sqs, typ)

Arguments

Value

list of ClstrRecs

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Cluster record contains all information on a cluster.

Usage

## S4 method for signature 'ClstrRec'
as.character(x)

## S4 method for signature 'ClstrRec'
show(object)

## S4 method for signature 'ClstrRec'
print(x)

## S4 method for signature 'ClstrRec'
str(object, max.level = 2L, ...)

## S4 method for signature 'ClstrRec'
summary(object)

Arguments

Slots

id

Cluster ID, integer

sids

Sequence IDs

nsqs

Number of sequences

txids

Source txids for sequences

ntx

Number of taxa

typ

Cluster type: direct, subtree or merged

seed

Seed sequence ID

prnt

Parent taxonomic ID

See Also

Other run-public: ClstrArc-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

data('aotus')
clstrrec <- aotus@clstrs@clstrs[[1]]
# this is a ClstrRec object
# it contains cluster information
show(clstrrec)
# you can access its different data slots with @
clstrrec@id     # cluster id
clstrrec@sids   # sequence IDs
clstrrec@nsqs   # number of sequences
clstrrec@txids  # taxonomic IDs of sequences
clstrrec@ntx    # number unique taxonomic IDs
clstrrec@typ    # cluster type: merged, subtree, direct or paraphyly
clstrrec@prnt   # MRCA of all taxa
clstrrec@seed   # most inter-connected sequence

Description

Loop through downloaded sequences for each clade and hierarchically find clusters using BLAST.

Usage

clstrs_calc(txdct, ps)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Uses seed sequence BLAST results and IDs to join clusters identified as sisters into single clusters. Resulting object is of joined clusters, merging is required to reformat the clusters for subsequent analysis.

Usage

clstrs_join(blast_res, seed_ids, all_clstrs, ps)

Arguments

Value

list of joined clusters

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Takes a list of joined clusters and computes each data slot to create a single merged cluster. txdct is required for parent look-up.

Usage

clstrs_merge(jnd_clstrs, txdct)

Arguments

Value

list of ClstrRecs

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Returns a ClstrArc with ID determined by the number of sequences in each cluster.

Usage

clstrs_renumber(clstrrecs)

Arguments

Value

ClstrArc

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Saves clusters generated by clstr_all to cache.

Usage

clstrs_save(wd, txid, clstrs)

Arguments

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Run the third stage of the phylotaR pipeline, cluster. This stage hierarchically traverses the taxonomy identifying all direct and subtree clusters from downloaded sequences. Any taxonomic nodes too small for cluster identification are placed into paraphyletic clusters.

Usage

clusters_run(wd)

Arguments

See Also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

## Not run: 
  
  # Note: this example requires BLAST and internet to run.
  
  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
    dir.create(wd)
  }
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # individually run stages
  taxise_run(wd = wd)
  download_run(wd = wd)
  clusters_run(wd = wd)

## End(Not run)

Description

Run the fourth stage of the phylotaR pipeline, cluster2. Identify clusters at higher taxonomic levels by merging sister clusters.

Usage

clusters2_run(wd)

Arguments

See Also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

## Not run: 
  
  # Note: this example requires BLAST and internet to run.
  
  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
    dir.create(wd)
  }
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # individually run stages
  taxise_run(wd = wd)
  download_run(wd = wd)
  clusters_run(wd = wd)
  clusters2_run(wd = wd)

## End(Not run)

Description

Provide the command and arguments as a vector. Also can take a lgfl to which all stdout and stderr is written. If lgfl is not provided, a list is returned of 'status', 'stdout' and 'stderr'. Else only the status is returned - 1 success, 0 failed.

Usage

cmdln(cmd, args, ps, lgfl = NULL)

Arguments

Details

Note, stdout/err are returned as 'raw'. Use rawToChar() to convert to characters.

Value

status, integer or character

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Return TreeMen of concatenated trees.

Usage

cTrees(x, ...)

Arguments

Details

Concatenate trees into single TreeMen object.

See Also

TreeMen-class, TreeMan-class, list-to-TreeMen

Examples

trees <- cTrees(randTree(10), randTree(10))

Description

cycads

Format

A TreeMan or Phylota object

Examples

data("cycads")

Description

Look-up either direct or all taxonomic descendants of a node from taxonomic dictionary.

Usage

descendants_get(id, txdct, direct = FALSE)

Arguments

Value

vector

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Returns T/F. Checks if object returned from rentrez function is as expected.

Usage

download_obj_check(obj)

Arguments

Value

T/F

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

Description

Run the second stage of phylotaR, download. This stage downloads sequences for all nodes with sequence numbers less than mxsqs. It hierarchically traverses the taxonomy for each node and downloads direct and subtree sequences for all descendants.

Usage

download_run(wd)

Arguments

Examples

## Not run: 
  
  # Note: this example requires BLAST and internet to run.
  
  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
    dir.create(wd)
  }
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # individually run stages
  taxise_run(wd = wd)
  download_run(wd = wd)

## End(Not run)

Description

dragonflies

Format

A TreeMan or Phylota object

Examples

data("dragonflies")

Description

Identifies higher level taxa for each sequence in clusters for given rank. Selects representative sequences for each unique taxon using the choose_by functions. By default, the function will choose the top ten sequences by first sorting by those with fewest number of ambiguous sequences, then by youngest, then by sequence length.

Usage

drop_by_rank(
  phylota,
  rnk = "species",
  keep_higher = FALSE,
  n = 10,
  choose_by = c("pambgs", "age", "nncltds"),
  greatest = c(FALSE, FALSE, TRUE)
)

Arguments

Value

phylota

See Also

Other tools-public: calc_mad(), calc_wrdfrq(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota(), write_sqs()

Examples

data("dragonflies")
# For faster computations, let's only work with the 5 clusters.
dragonflies <- drop_clstrs(phylota = dragonflies, cid = dragonflies@cids[10:15])


# We can use drop_by_rank() to reduce to 10 sequences per genus for each cluster
(reduced_1 <- drop_by_rank(phylota = dragonflies, rnk = 'genus', n = 10,
                           choose_by = c('pambgs', 'age', 'nncltds'),
                           greatest = c(FALSE, FALSE, TRUE)))

# We can specify what aspects of the sequences we would like to select per genus
# By default we select the sequences with fewest ambiguous nucleotides (e.g.
# we avoid Ns), the youngest age and then longest sequence.
# We can reverse the 'greatest' to get the opposite.
(reduced_2 <- drop_by_rank(phylota = dragonflies, rnk = 'genus', n = 10,
                           choose_by = c('pambgs', 'age', 'nncltds'),
                           greatest = c(TRUE, TRUE, FALSE)))


# Leading to smaller sequnces ...
r1_sqlngth <- mean(get_sq_slot(phylota = reduced_1,
                                sid = reduced_1@sids, slt_nm = 'nncltds'))
r2_sqlngth <- mean(get_sq_slot(phylota = reduced_2,
                                sid = reduced_2@sids, slt_nm = 'nncltds'))
(r1_sqlngth > r2_sqlngth)
# ... with more ambigous characters ....
r1_pambgs <- mean(get_sq_slot(phylota = reduced_1, sid = reduced_1@sids,
                              slt_nm = 'pambgs'))
r2_pambgs <- mean(get_sq_slot(phylota = reduced_2, sid = reduced_2@sids,
                              slt_nm = 'pambgs'))
(r1_pambgs < r2_pambgs)
# .... and older ages (measured in days since being added to GenBank).
r1_age <- mean(get_sq_slot(phylota = reduced_1, sid = reduced_1@sids,
                           slt_nm = 'age'))
r2_age <- mean(get_sq_slot(phylota = reduced_2, sid = reduced_2@sids,
                           slt_nm = 'age'))
(r1_age < r2_age)


# Or... we can simply reduce the clusters to just one sequence per genus
(dragonflies <- drop_by_rank(phylota = dragonflies, rnk = 'genus', n = 1))

Description

Drops all clusters except those identified by user.

Usage

drop_clstrs(phylota, cid)

Arguments

Value

phylota

See Also

Other tools-public: calc_mad(), calc_wrdfrq(), drop_by_rank(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota(), write_sqs()

Examples

data("dragonflies")
# specify cids to *keep*
random_cids <- sample(dragonflies@cids, 100)
# drop an entire cluster
nbefore <- length(dragonflies@cids)
dragonflies <- drop_clstrs(phylota = dragonflies, cid = random_cids)
nafter <- length(dragonflies@cids)
# now there are only 100 clusters
(nafter < nbefore)

Description

Drop all sequences in a cluster except those identified by user.

Usage

drop_sqs(phylota, cid, sid)

Arguments