Changelog
Source:NEWS.md
MiscMetabar 0.7 (in development)
Add functions
chimera_detection_vs()
andchimera_removal_vs()
to process chimera detection and removal using vsearch softwareAdd functions
filter_trim()
,sample_data_with_new_names()
andrename_samples()
to facilitate the use of targets for bioinformatic pipeline.Add function
add_info_to_sam_data()
to expand sam_data slot using a data.frame and using nb_asv and nb_seqAdd functions
swarm_clustering()
andvsearch_clustering()
and addswarm
method in the functionasv2otu()
Add function
physeq_or_string_to_dna()
mostly for internal useAdd function
cutadapt_remove_primers()
to remove primers using cutadaptAdd internal functions
is_swarm_installed()
,is_cutadapt_installed()
,is_vsearch_installed()
andis_falco_installed()
to test for the availability of external software in order to run examples and test from testthat.Submit to CRAN and change code to comply with their rules (patch 0.7.1 to 0.7.8)
Numerous examples and tests are skipped on CRAN because it spends to much time to run. Rules vignettes is updated to details the strategy for this.
BREAKING CHANGES
- Harmonization of parameters names:
-
add_nb_sequences
->add_nb_seq
inggvenn_pq()
-
db
->db_url
inget_funguild_db()
-
db
->db_funguild
inget_funguild_db()
-
file
->file_path
inget_file_extension()
-
n_seq
->nb_seq
insubsample_fastq()
-
otutable
->otu_table
inlulu()
-
alpha
->pval
inplot_edgeR_pq()
andplot_deseq2_pq()
and change default value from 0.01 to more classical 0.05 -
sequences
->seq2search
in functionsearch_exact_seq_pq()
-
seq_names
->dna_seq
in functionasv2otu
-
MiscMetabar 0.6.0
- Add function
ancombc_pq()
to simplify the call toANCOMBC::ancombc2()
: ANalysis of COmpositions of Microbiomes with Bias Correction 2 - Add param
taxa_names_from_physeq
(default FALSE) tosubset_taxa_pq()
- Add param
rarefy_by_sample
(default FALSE) to functionggbetween_pq()
- Add function
are_modality_even_depth()
to test if samples depth significantly vary among the modalities of a factor - Add functions
merge_taxa_vec()
andmerge_samples2()
from the speedyseq package into MiscMetabar to decrease package dependencies (Thanks to Mike R. Mclaren) - Add function
reorder_taxa_pq()
in order to replace the unique call to package MicroViz to decrease package dependencies. - Add functions
get_funguild_db()
andfunguild_assign()
from the FUNGuildR package into MiscMetabar to decrease package dependencies - Remove all dependencies from packages not available on CRAN or Bioconductor. Improve code using
goodpractice::gp
() anddevtools::check()
function - Add messages in various cases (NA in samples data, low number of sequences in samples, low number of sequences by taxa) when using
verify_pq()
with argsverbose=TRUE
- Fix a bug in
multitax_bar_pq()
when usingnb_seq = FALSE
MiscMetabar 0.52
- Add function
ggbetween_pq()
to facilitate comparison of hill number using the power ofggstatsplot::ggbetweenstats()
- Add function
plot_SCBD_pq()
to plot species contributions to beta diversity (SCBD) of samples
MiscMetabar 0.51
- Add function
LCBD_pq()
andplot_LCBD_pq()
to compute, test and plot local contributions to beta diversity (LCBD) of samples - Add function
tbl_sum_samdata()
to summarize information from sample data in a table - Add function
mumu_pq()
to use mumu, a fast and robust C++ implementation of lulu. - Add (a mostly internal) function
install_pkg_needed()
to install pkg (mostly for package list in Suggest in DESCRIPTION) if needed by a function. - Add function
add_funguild_info()
andplot_guild_pq()
to add and plot fungal guild information from taxonomy usingFUNGuild
package - Add function
build_phytree_pq()
to build 3 phylogenetic trees (NJ, UPGMA and ML usingphangorn
R package) from therefseq
slot of aphyloseq
object, possibly with bootstrap values. See the vignettes Tree visualization for an introduction to tree visualization usingggtree
R package.
MiscMetabar 0.5
- Phyloseq object are converted in taxa_are_columns in the
ggvenn_pq()
thanks to issue #31
BREAKING CHANGES
- Rename param
log_10
in functionbiplot_pq()
intolog10trans
- Rename param
log10transform
in functioncircle_pq()
intolog10trans
MiscMetabar 0.42
- Add argument
one_plot
(default FALSE, same behavior than before) tohill_pq
function in order to return an unique ggplot2 object with the four plots inside. - Add argument
correction_for_sample_size
(default TRUE, same behavior than before) tohill_pq
andhill_tuckey_pq
function to allow removing any correction for uneven sampling depth. - Add function
multitax_bar_pq()
to plot 3 levels of taxonomy in function of samples attributes - Add function
ridges_pq()
to plot ridges of one taxonomic level in function of samples attributes - Add function
treemap_pq
to plot treemap of two taxonomic levels
MiscMetabar 0.41
- Add function
iNEXT_pq()
to calculate hill diversity using the iNEXT package. - Add argument
pairs
tomulti_biplot_pq()
in order to indicate all pairs of samples we want to print. - Improve
compare_pairs_pq()
with information about the number of shared sequences among pairs. - Add function
upset_pq()
to plot upset of phyloseq object using the ComplexUpset package. - Add function
upset_test_pq
to test for differences between intersections (wrapper ofComplexUpset::upset_test()
forphyloseq-object
). - Add info (param
add_info
) in subtitle of thehill_pq()
function. - Add argument
remove_space
tosimplify_taxo()
function. - Add argument
simplify_taxo
toclean_pq()
function. - Change argument
rarefy_nb_seq
byrarefy_before_merging
and add argumentsrarefy_after_merging
andadd_nb_seq
toggvenn_pq()
function. - Add arguments
rarefy_after_merging
tobiplot_pq()
andupset_pq()
functions. - Add argument
taxa_fill
toupset_pq()
function in order to fill the bar with taxonomic rank. - Add a function
subsample_fastq()
to make subset of fastq files in order to test your pipeline with all samples but with a low number of reads. - Add a function
accu_samp_threshold()
to compute the number of sequence to obtain a given proportion of ASV in accumulation curves (`accu_plot). - Add a function
tax_bar_pq()
in order to plot taxonomic distribution across samples.
MiscMetabar 0.40
- Add function
multi_biplot_pq()
to visualize a collection of couples of samples for comparison through a list ofbiplot_pq()
. - Add options
add_info
,na_remove
, andclean_pq
toplot_tax_pq()
function. - Add options
vsearch_cluster_method
andvsearch_args
tootu2asv()
for more detailed control of the vsearch software. - Suppression of buggy function
MM_idtaxa()
. - Add a wrapper of
write_pq()
calledsave_pq()
to save a phyloseq object in the three possible formats () at the same time- 4 separate tables
- 1 table version
- 1 RData file
- Add a function
add_blast_info()
to add information fromblast_pq()
to thetax_table
slot of a phyloseq object. - Add option
keep_temporary_files
inasv2otu()
function. - Improve the documentation of
asv2otu()
and fix a little bug in the name of the conserved ASV afterasv2otu()
. - Test coverage largely improved leading to numerous minor bug fixes.
- Add function
search_exact_seq_pq()
to search for exact matching of sequences using complement, reverse and reverse-complement against a phyloseq object. - Add function
add_new_taxonomy_pq()
to add new taxonomic rank to a phyloseq object. For example to add taxonomic assignment from a new database. - Add a battery of test using
test_that
package and improve code compatibility with cran recommendations.
BREAKING CHANGES
-
asv2otu()
withmethod="vsearch"
change two default values (to repeat the precedent behavior, useasv2otu(..., vsearch_cluster_method = "--cluster_fast", tax_adjust = 1)
):- vsearch_cluster_method = “–cluster_size”
- tax_adjust = 0
MiscMetabar 0.34
- Add option
add_nb_samples
toggvenn_pq()
which add the number of samples to level name in the plot. Useful to see disequilibrium in the number of samples among the factor’s levels. - Add option
args_makedb
andargs_blastn
to functionsblast_pq()
,blast_to_phyloseq()
,blast_to_derep()
andfilter_asv_blast()
. - Add option
rarefy_nb_seqs
toggven_pq()
in order to rarefy samples before plotting. - Add function
SRS_curve_pq()
to plot scaling with ranked subsampling (SRS) curves using theSRS::SRS_curve()
function (see citation(“SRS”) for reference). - Add option
nb_samples_info
tobiplot_pq()
in order to add the number of samples merged by level of factors. - Add a message when two modalities differ greatly (more than x2) in their number of sequences in
biplot_pq()
andggvenn_pq()
. - Add options
na_remove
,dist_method
(including Aitchinson and robust-Aitchinson distance),correction_for_sample_size
andrarefy_nb_seqs
options toadonis_pq()
function. - Add option
na_remove
tograph_test_pq()
function.
MiscMetabar 0.33
- Add function
plot_tax_pq()
to plot taxonomic distribution (nb of sequences or nb of ASV) across factor. - Add option
add_points
and make better axis ofhill_pq()
function - Add function
blast_to_derep()
in order to facilitate searching some fasta sequences in dereplicated sequences (obtained bydada2::derepFastq
)
Database (makeblastdb) | Sequences to blast (blastn) | |
---|---|---|
blast_to_phyloseq() |
Built from ref_seq slot(physeq-class) |
Custom fasta file |
blast_to_derep() |
Built from dereplicate sequences (derep-class) | Custom fasta file |
blast_pq() |
Custom database or custom fasta file |
ref_seq slot of a physeq object |
- Add functions
tsne_pq()
andplot_tsne_pq()
to quickly visualize results of the t-SNE multidimensional analysis based on theRtsne::Rtsne()
function.
MiscMetabar 0.32
- Add the possibility to select a folder in the function
count_seq()
- Add functions
track_wkflow_samples()
andselect_one_sample()
- Add option
sam_data_first
in functionwrite_pq()
- Add option
reorder_asv
andrename_asv
to in functionwrite_pq()
andclean_pq
- Add a function
rotl_pq()
to build a phylogenetic tree using the ASV binomial names of a physeq object and the Open Tree of Life tree.
MiscMetabar 0.31
- Argument
split_by
to make multiple plot given a variable insam_data
slot (functionggvenn_pq()
) - Argument
seq_names
inasv2otu()
function allow to clusterize sequences from a character vector of DNA. - Add a
blast_pq()
function to blast the sequences of the@ref_seq
slot against a custom database - Add a
filter_asv_blast()
function to filter ASV in phyloseq dataset using blast against a custom database - Add a
subset_taxa_pq()
function to filter ASV based on a named conditional vector. Used infilter_asv_blast()
. - Add parameter
force_taxa_as_columns
(default FALSE) andforce_taxa_as_rows
(default FALSE) toclean_pq()
. - Add a first version of the function
count_fastq_seq()
to count sequences from fastq.gz files directly from R. - Add taxonomic info to
track_wkflow()
function (parametertaxonomy_rank
)
MiscMetabar 0.3
- Change some function names, mainly replacing
physeq
bypk
. - Improve documentation using some rules documented in the Rules vignettes.
- Add a option
sam_names()
toread_pq()
- Correction of
data_fungi
anddata_fungi_sp_known
metadata
MiscMetabar 0.24
- Add supplementary info in summary_plot_physeq()`
- Better arguments in biplot_physeq()`)
- Add merge_sample_by argument in biplot_physeq()`
- Better documentation with more example.
- For other minors bugs fixes and addition, see the list of commits
MiscMetabar 0.23
Adapt the function
asv2otu()
to IdClusters change in the DECIPHER package (commit 254100922f2093cc789d018c18a26752a3cda1e3). Then change the IdClusters function that was removed from DECIPHER to Clusterize function.Better functioning of
blast_to_phyloseq()
when none query sequences are founded.Add tax_adjust argument to
asv2otu()
functionAdd some functions useful for the targets package
Add a
biplot_physeq()
function to visualize of two samples for comparison of physeq objectAdd an argument modality in the
tax_datatable()
function to split OTU abundancy by level of the sample modalityAdd a function
multiple_share_bisamples()
to help compare samples by pairsAdd a new function (
ggVenn_phyloseq()
) for better venn diagram but without area calculation (usevenn_phyloseq()
in this case).Add two functions helpful for beta-diversity analysis (
adonis_phyloseq()
andphyseq_graph_test()
)
MiscMetabar 0.22
- Add badge to set the development lifecycle of each function
- Add the lulu_phyloseq function to make easy the reclustering of phyloseq object using the lulu algorithm (https://www.nature.com/articles/s41467-017-01312-x) from the lulu package.