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Merge pull request #106 from adrientaudiere/dev
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adrientaudiere authored Nov 28, 2024
2 parents 2c4553b + 4d618f8 commit 10ec9d0
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -15,3 +15,4 @@
^citation.cff$
^vignettes/articles$
^cran-comments\.md$
^.lintr
6 changes: 3 additions & 3 deletions .github/workflows/test-coverage.yaml
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Expand Up @@ -36,7 +36,7 @@ jobs:
&& cd ./mumu/ \
&& make \
&& make check \
&& sudo make install
&& sudo make install
- name: Install swarm
run: |
Expand Down Expand Up @@ -67,11 +67,11 @@ jobs:

- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package
- name: Upload coverage reports to Codecov with GitHub Action
uses: codecov/[email protected]
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
3 changes: 2 additions & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Package: MiscMetabar
Type: Package
Title: Miscellaneous Functions for Metabarcoding Analysis
Version: 0.10.3
Version: 0.10.4
Authors@R: person("Adrien", "Taudière", email = "[email protected]",
role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Expand Down Expand Up @@ -44,6 +44,7 @@ Suggests:
httr,
iNEXT,
indicspecies,
IRanges,
jsonlite,
knitr,
magrittr,
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -94,6 +94,8 @@ export(plot_edgeR_phyloseq)
export(plot_edgeR_pq)
export(plot_guild_pq)
export(plot_mt)
export(plot_refseq_extremity_pq)
export(plot_refseq_pq)
export(plot_tax_pq)
export(plot_tsne_pq)
export(plot_var_part_pq)
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10 changes: 8 additions & 2 deletions NEWS.md
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@@ -1,10 +1,16 @@
# MiscMetabar 0.10.3 (in development)
# MiscMetabar 0.10.5 (in development)

# MiscMetabar 0.10.4

- Add functions `plot_refseq_pq()` and `plot_refseq_extremity_pq()` to plot the proportion of each nucleotide and the diversity of nucleotides from `@refseq` of a phyloseq object.

# MiscMetabar 0.10.3

- Add params `type`, `na_remove` and `verbose` to `ggvenn_pq()`. The type = "nb_seq" allow to plot Venn diagram with the number of shared sequences instead of shared ASV.
- Add automatic report in json for the function `cutadapt_remove_primers()`.
- Add param `verbose` to `track_wkflow()` and improve examples for `track_wkflow()` and `list_fastq_files`

# MiscMetabar 0.10.2 (in development)
# MiscMetabar 0.10.2

- Improve code thanks to {lintr} package
- Add option `return_file_path` to `cutadapt_remove_primers()` in order to facilitate targets pipeline
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3 changes: 2 additions & 1 deletion R/MiscMetabar-package.R
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Expand Up @@ -25,7 +25,8 @@ if (getRversion() >= "2.15.1") {
"ymin", ".group", "archetype", "nOTUid", "taxon", "total",
"chim_rm", "condition", "physeq", "seq_tab_Pairs", "nb_samp", "silent",
"X1_lim1", "X1_lim2", "aicc", "variable", "pos_letters", "alluvium",
"na_remove", "stratum", "to_lodes_form"
"na_remove", "stratum", "to_lodes_form", "clean_fastq", "clean_sam",
"samples_names_common", "seq_id"
))
}

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9 changes: 5 additions & 4 deletions R/dada_phyloseq.R
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Expand Up @@ -226,6 +226,7 @@ clean_pq <- function(physeq,
#' @param taxonomy_rank A vector of int. Define the column number of
#' taxonomic rank `in physeq@tax_table` to compute the number of unique value.
#' Default is NULL and do not compute values for any taxonomic rank
#' @param verbose (logical) If true, print some additional messages.
#' @param ... Other arguments passed on to [clean_pq()] function.
#'
#' @return The number of sequences, clusters (e.g. OTUs, ASVs) and samples for
Expand Down Expand Up @@ -1032,8 +1033,8 @@ read_pq <- function(path = NULL,
#' Set to number of cpus/processors to use for the clustering
#' @param id (default: 0.84) id for --usearch_global.
#' @param vsearchpath (default: vsearch) path to vsearch.
#' @param verbose (logical) if true, print some additional messages.
#' @param clean_pq (logical) if true, empty samples and empty ASV are discarded
#' @param verbose (logical) If true, print some additional messages.
#' @param clean_pq (logical) If true, empty samples and empty ASV are discarded
#' before clustering.
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary files
#' @param ... Others args for function [lulu()]
Expand Down Expand Up @@ -1188,8 +1189,8 @@ lulu_pq <- function(physeq,
#' @param vsearchpath (default: vsearch) path to vsearch.
#' @param mumupath path to mumu. See [mumu](https://github.com/frederic-mahe/mumu)
#' for installation instruction
#' @param verbose (logical) if true, print some additional messages.
#' @param clean_pq (logical) if true, empty samples and empty ASV are discarded
#' @param verbose (logical) If true, print some additional messages.
#' @param clean_pq (logical) If true, empty samples and empty ASV are discarded
#' before clustering.
#' @param keep_temporary_files (logical, default: FALSE) Do we keep temporary files
#' @return a list of for object
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