- Homogenize terminology replacing ASV by taxa/taxon in documentation and code
- Build an alias function
filter_taxa_blast()
forfilter_asv_blast()
- Build an alias function
postcluster_pq()
forasv2otu()
- Replacing misnamed param
rename_asv
byrename_taxons
inclean_pq()
- Replacing misnamed param
reorder_asv
byreorder_taxons
inclean_pq()
- Add param
default_fun
in functionmerge_samples2()
in order to replace the default function that change the sample data in case of merging. A useful parameter isdefault_fun=diff_fct_diff_class
. - Add param
kruskal_test
tohill_pq()
function to prevent user to mis-interpret Tuckey HSD result (and letters) if the global effect of the tested factor on Hill diversity is non significant. - Add param
vioplot
to hill_pq() function to allow violin plot instead of boxplot. - Modify
rarefy_sample_count_by_modality
to debug the case of modality with level of length one.
- Add functions
taxa_as_rows()
andtaxa_as_columns()
to replace verbose called toclean_pq()
- Add function
ggscatt_pq()
to plot and test for effect of a numerical columns in sam_data on Hill number. Its the equivalent for numerical variables ofggbetween_pq()
which focus on the effect of a factor. - Add functions
var_par_pq()
,var_par_rarperm_pq()
andplot_var_part_pq()
to compute the partition of the variation of community and plot it. It introduce the notion ofrarperm
part in the function name. It refers to the fact that this function compute permutation of samples depth rarefaction to measure the variation due to the random process in rarefaction. - Add function
hill_test_rarperm_pq()
to test the effect of a factor on hill diversity accounting for the variation due to random nature of the rarefaction by sample depth. - Add function
rarefy_sample_count_by_modality()
to equalize the number of samples for each levels of a modality (factor) - Add function
accu_plot_balanced_modality()
to plot accumulation curves with balanced modality (same number of samples per level) and depth rarefaction (same number of sequences per sample) - Add function
adonis_rarperm_pq()
to compute multiple Permanova analyses on different sample depth rarefaction. - Add function
ggaluv_pq()
to plot taxonomic distribution in alluvial fashion with ggplot2 (using the [ggalluvial] package) - Add function
glmutli_pq()
to use automated model selection and multimodel inference with (G)LMs for phyloseq object
- Add param
taxa_ranks
in functionpsmelt_samples_pq()
to group results by samples AND taxonomic ranks. - Add param
hill_scales
in functionshill_tuckey_pq()
andhill_p()
to choose the level of the hill number. - Add param
na_remove
in functionhill_pq()
to remove samples with NA in the factor fact.
- Add param
plot_with_tuckey
tohill_pq()
., - Add function
formattable_pq()
to make beautiful table of the distribution of taxa across a modality using visualization inside in the table. - Add functions
fac2col()
andtransp()
to facilitate manipulation of colors, especially in functionformattable_pq()
- Add functions
signif_ancombc()
andplot_ancombc_pq()
to plot significant results fromancombc_pq()
function - Add function
distri_1_taxa()
to summarize the distribution of one given taxa across level of a modality - Add function
normalize_prop_pq()
to implement the method proposed by McKnight et al. 2018 - Add function
psmelt_samples_pq()
to build data frame of samples information including the number of sequences (Abundance) and Hill diversity metrics. Useful to use with the ggstatsplot packages (see examples). - Replace param
variable
byfact
in functionggbetween_pq()
andhill_pq()
(keeping the variable option inhill_pq()
for backward compatibility) - Fix a bug in the class of the return object of function
chimera_removal_vs()
. Now it return a matrix to be able to be parsed on to [dada2::getUniques()]
-
Add functions
chimera_detection_vs()
andchimera_removal_vs()
to process chimera detection and removal using vsearch software -
Add 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_seq -
Add functions
swarm_clustering()
andvsearch_clustering()
and addswarm
method in the functionasv2otu()
-
Add function
physeq_or_string_to_dna()
mostly for internal use -
Add function
cutadapt_remove_primers()
to remove primers using cutadapt -
Add 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 0.7.9)
-
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.
-
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 0.05sequences
->seq2search
in functionsearch_exact_seq_pq()
seq_names
->dna_seq
in functionasv2otu
-
Removing the function
install_pkg_needed()
which do not comply with CRAN policies
- 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
- 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
- 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.
- Phyloseq object are converted in taxa_are_columns in the
ggvenn_pq()
thanks to issue #31
- Rename param
log_10
in functionbiplot_pq()
intolog10trans
- Rename param
log10transform
in functioncircle_pq()
intolog10trans
- 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
- 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.
- 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.
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
- 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.
- 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.
- 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.
- 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
)
- Change some function names, mainly replacing
physeq
bypk
. \tabular{rl}{graph_test_pq()
\tab now a synonym forphyseq_graph_test
\cradonis_pq()
\tab now a synonym foradonis_phyloseq
\crclean_pq()
\tab now a synonym forclean_physeq
\crlulu_pq()
\tab now a synonym forlulu_phyloseq
\crcircle_pq()
\tab now a synonym forotu_circle
\crbiplot_pq()
\tab now a synonym forbiplot_physeq
\crread_pq()
\tab now a synonym forread_phyloseq
\crwrite_pq()
\tab now a synonym forwrite_phyloseq
\crsankey_pq()
\tab now a synonym forsankey_phyloseq
\crsummary_plot_pq()
\tab now a synonym forsummary_plot_phyloseq
\crplot_edgeR_pq()
\tab now a synonym forplot_edgeR_phyloseq
\crplot_deseq2_pq()
\tab now a synonym forplot_deseq2_phyloseq
\crvenn_pq()
\tab now a synonym forvenn_phyloseq
\crggvenn_pq()
\tab now a synonym forggVenn_phyloseq
\crhill_tuckey_pq()
\tab now a synonym forhill_tuckey_phyloseq
\crhill_pq()
\tab now a synonym forhill_phyloseq
\crheat_tree_pq()
\tab now a synonym forphyseq_heat_tree
\crcompare_pairs_pq()
\tab now a synonym formultiple_share_bisamples
\cr } - 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
- 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
-
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()
function -
Add some functions useful for the targets package
-
Add a
biplot_physeq()
function to visualize of two samples for comparison of physeq object -
Add an argument modality in the
tax_datatable()
function to split OTU abundancy by level of the sample modality -
Add a function
multiple_share_bisamples()
to help compare samples by pairs -
Add 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()
)
- 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.
- This is the first release of pkgdown.