Last updated: 2020-05-15
Checks: 4 3
Knit directory: SolFaMi_bioinfo/
This reproducible R Markdown analysis was created with workflowr (version 1.6.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
The global environment had objects present when the code in the R Markdown file was run. These objects can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment. Use wflow_publish or wflow_build to ensure that the code is always run in an empty environment.
The following objects were defined in the global environment when these results were created:
| Name | Class | Size |
|---|---|---|
| add_dna_to_phyloseq | function | 7.6 Kb |
| asv2otu | function | 23.7 Kb |
| dada_to_phyloseq | function | 1.8 Kb |
| drake_envir | environment | 56 bytes |
| funguild_from_taxo | function | 27.1 Kb |
| list_fastq_files | function | 10.2 Kb |
| plan | drake_plan;tbl_df;tbl;data.frame | 21.1 Kb |
| quality_filter_fastp | function | 19.7 Kb |
| quality_report | function | 336 bytes |
| remove_chimera | function | 2.5 Kb |
| rename_sample | function | 6.7 Kb |
| sample_data_matching | function | 3.2 Kb |
| taxo_from_seqtab | function | 2.5 Kb |
| track_wkflow | function | 57.6 Kb |
The command set.seed(20200401) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
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To ensure reproducibility of the results, delete the cache directory Bioinfo_cache and re-run the analysis. To have workflowr automatically delete the cache directory prior to building the file, set delete_cache = TRUE when running wflow_build() or wflow_publish().
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The results in this page were generated with repository version aab21dc. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
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Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: .drake/config/
Ignored: .drake/data/
Ignored: .drake/drake/
Ignored: .drake/keys/
Ignored: .drake/scratch/
Ignored: analysis/Bioinfo_cache/
Ignored: data/raw_seq/
Ignored: output/filterAndTrim_fwd/
Ignored: output/filterAndTrim_rev/
Ignored: renv/library/
Ignored: renv/staging/
Unstaged changes:
Modified: .workInProgress.Rmd
Modified: analysis/Bioinfo.Rmd
Modified: analysis/_site.yml
Modified: code/plan.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Bioinfo.Rmd) and HTML (public/Bioinfo.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 08ab169 | adrientaudiere | 2020-05-15 | Add report to drake plan and new physeq objects with re-clusterisation |
| Rmd | 006a4e7 | adrientaudiere | 2020-05-12 | Add _drake.R and plan.R allowing the use of r_make |
| Rmd | 73a6a6a | adrientaudiere | 2020-05-12 | New drake plan |
| Rmd | be2d56f | adrientaudiere | 2020-05-08 | ammend plan_ligth and try a first plan with all files |
| Rmd | 40fb4ef | adrientaudiere | 2020-05-07 | make a plan_ligth plan to test the transform argument of target function |
| Rmd | be05791 | adrientaudiere | 2020-05-07 | Add target and use format = “qs” to save big object |
| Rmd | 2b5702d | adrientaudiere | 2020-05-06 | First try with the entire dataset |
| Rmd | 9ab379b | adrientaudiere | 2020-05-06 | Better plan |
| Rmd | 7adc02c | adrientaudiere | 2020-05-04 | first drake version on a subset of fastq files |
| Rmd | 6b478fe | adrientaudiere | 2020-04-28 | update nav links |
| html | 6b478fe | adrientaudiere | 2020-04-28 | update nav links |
| html | a1f274a | adrientaudiere | 2020-04-28 | Build site. |
| Rmd | 2a1f393 | adrientaudiere | 2020-04-28 | workflowr::wflow_publish(all = T) |
| Rmd | b5a3cac | adrientaudiere | 2020-04-28 | Update package |
| html | f9f6bd8 | adrientaudiere | 2020-04-28 | Build site. |
| Rmd | 81e0125 | adrientaudiere | 2020-04-28 | try publish 2 |
| html | 302cf0c | adrientaudiere | 2020-04-28 | Build site. |
| Rmd | cdde2f0 | adrientaudiere | 2020-04-28 | Add analysis files |
The _drake.R make the drake plan after sourcing code/packages.R, code/functions_bioinfo.R and code/plan.R.
source("_drake.R")* The lockfile is already up to date.# r_make() # need to run r_make if you change the plan
Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.
vis_drake_graph(plan, envir = drake_envir)
Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.
track <- track_wkflow(
list(
"raw_data_fw" = normalizePath(readd(data)$fnfs),
"raw_data_rev" = normalizePath(readd(data)$fnrs),
"filter_data_fw" = normalizePath(
list.files("output/filterAndTrim_fwd/",
full.names = TRUE)),
"filter_data_rev" = normalizePath(
list.files("output/filterAndTrim_rev/",
full.names = TRUE)),
"derep_fs" = readd(derep_fs),
"derep_rs" = readd(derep_rs),
"ddR" = readd(ddR),
"ddF" = readd(ddF),
"merged_seq" = readd(merged_seq),
"seqtab_chim" = readd(seqtab_w_short_seq),
"seqtab" = readd(seqtab),
"data_phyloseq" = readd(data_phyloseq),
"data_phyloseq_otu" = readd(data_phyloseq_otu),
"data_phyloseq_otu_vsearch" = readd(data_phyloseq_otu_vsearch)
)
)Compute the number of sequencesStart object of class: character
Start object of class: character
Start object of class: character
Start object of class: characterStart object of class: list
Start object of class: list
Start object of class: list
Start object of class: list
Start object of class: listStart object of class: matrix
Start object of class: matrixStart object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseqCompute the number of clustersStart object of class: character
Start object of class: character
Start object of class: character
Start object of class: characterStart object of class: list
Start object of class: list
Start object of class: list
Start object of class: list
Start object of class: listStart object of class: matrix
Start object of class: matrixStart object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseqCompute the number of samplesStart object of class: character
Start object of class: character
Start object of class: character
Start object of class: characterStart object of class: list
Start object of class: list
Start object of class: list
Start object of class: list
Start object of class: listStart object of class: matrix
Start object of class: matrixStart object of class: phyloseq
Start object of class: phyloseq
Start object of class: phyloseq
Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.
track_formattable <- track
track_formattable$nb_singletons <- NA
track_formattable[c("derep_fs", "derep_rs"),]$nb_singletons <-
track_formattable[c("derep_fs", "derep_rs"),]$nb_clusters
track_formattable[c("derep_fs", "derep_rs"),]$nb_clusters <- NA
track_formattable[is.na(track_formattable)] <- ""
formattable(track_formattable,
list(
area(col = nb_sequences) ~ color_bar("cyan", na.rm = T),
area(col = nb_clusters) ~ normalize_bar("yellowgreen", na.rm = TRUE),
area(col = nb_singletons) ~ color_tile("orange", "orange"),
area(col = nb_samples) ~ color_tile("red", "pink")
)
)| nb_sequences | nb_clusters | nb_samples | nb_singletons | |
|---|---|---|---|---|
| raw_data_fw | 18929458 | 96 | ||
| raw_data_rev | 18929458 | 96 | ||
| filter_data_fw | 16595729 | 96 | ||
| filter_data_rev | 16595729 | 96 | ||
| derep_fs | 16595729 | 96 | 2608188 | |
| derep_rs | 16595729 | 96 | 2081688 | |
| ddR | 16572308 | 1398 | 96 | |
| ddF | 16540730 | 4148 | 96 | |
| merged_seq | 16524311 | 9637 | 96 | |
| seqtab_chim | 9063976 | 1446 | 96 | |
| seqtab | 9030839 | 1295 | 96 | |
| data_phyloseq | 9030839 | 1295 | 96 | |
| data_phyloseq_otu | 9030839 | 304 | 96 | |
| data_phyloseq_otu_vsearch | 9030839 | 250 | 96 |
Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: KDE neon User Edition 5.18
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8
[4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils methods base
other attached packages:
[1] knitr_1.28 tidyselect_1.0.0 speedyseq_0.1.2.9004 DECIPHER_2.14.0 RSQLite_2.2.0
[6] Biostrings_2.54.0 XVector_0.26.0 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[11] phyloseq_1.30.0 dada2_1.14.1 pbapply_1.4-2 formattable_0.2.0.1 dplyr_0.8.5
[16] styler_1.3.2 qs_0.21.2 ggraph_2.0.2 networkD3_0.4 here_0.1
[21] lubridate_1.7.8 visNetwork_2.0.9 forcats_0.5.0 readxl_1.3.1 Rcpp_1.0.4.6
[26] drake_7.12.0 devtools_2.3.0 usethis_1.6.0 BiocManager_1.30.10 gridExtra_2.3
[31] ggplot2_3.3.0 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] backports_1.1.6 plyr_1.8.6 igraph_1.2.5
[4] splines_3.6.3 storr_1.2.1 RApiSerialize_0.1.0
[7] BiocParallel_1.20.1 GenomeInfoDb_1.22.1 digest_0.6.25
[10] foreach_1.5.0 htmltools_0.4.0 viridis_0.5.1
[13] fansi_0.4.1 magrittr_1.5 memoise_1.1.0
[16] base64url_1.4 cluster_2.1.0 remotes_2.1.1
[19] graphlayouts_0.7.0 RcppParallel_5.0.0 matrixStats_0.56.0
[22] prettyunits_1.1.1 jpeg_0.1-8.1 colorspace_1.4-1
[25] blob_1.2.1 ggrepel_0.8.2 xfun_0.13
[28] callr_3.4.3 crayon_1.3.4 RCurl_1.98-1.2
[31] jsonlite_1.6.1 survival_3.1-12 iterators_1.0.12
[34] ape_5.3 glue_1.4.0 polyclip_1.10-0
[37] gtable_0.3.0 zlibbioc_1.32.0 DelayedArray_0.12.3
[40] pkgbuild_1.0.7 Rhdf5lib_1.8.0 scales_1.1.0
[43] DBI_1.1.0 viridisLite_0.3.0 progress_1.2.2
[46] bit_1.1-15.2 txtq_0.2.0 htmlwidgets_1.5.1
[49] RColorBrewer_1.1-2 ellipsis_0.3.0 pkgconfig_2.0.3
[52] farver_2.0.3 utf8_1.1.4 rlang_0.4.5
[55] reshape2_1.4.4 later_1.0.0 munsell_0.5.0
[58] cellranger_1.1.0 tools_3.6.3 cli_2.0.2
[61] generics_0.0.2 ade4_1.7-15 evaluate_0.14
[64] biomformat_1.14.0 stringr_1.4.0 yaml_2.2.1
[67] bit64_0.9-7 processx_3.4.2 fs_1.4.1
[70] tidygraph_1.1.2 purrr_0.3.4 nlme_3.1-147
[73] whisker_0.4 compiler_3.6.3 rstudioapi_0.11
[76] filelock_1.0.2 png_0.1-7 testthat_2.3.2
[79] tibble_3.0.1 tweenr_1.0.1 stringi_1.4.6
[82] highr_0.8 ps_1.3.2 desc_1.2.0
[85] lattice_0.20-41 Matrix_1.2-18 permute_0.9-5
[88] vegan_2.5-6 multtest_2.42.0 vctrs_0.2.4
[91] pillar_1.4.3 lifecycle_0.2.0 data.table_1.12.8
[94] bitops_1.0-6 httpuv_1.5.2 GenomicRanges_1.38.0
[97] R6_2.4.1 latticeExtra_0.6-29 hwriter_1.3.2
[100] promises_1.1.0 renv_0.9.3 ShortRead_1.44.3
[103] sessioninfo_1.1.1 codetools_0.2-16 MASS_7.3-51.6
[106] assertthat_0.2.1 pkgload_1.0.2 rhdf5_2.30.1
[109] SummarizedExperiment_1.16.1 rprojroot_1.3-2 withr_2.2.0
[112] GenomicAlignments_1.22.1 Rsamtools_2.2.3 GenomeInfoDbData_1.2.2
[115] mgcv_1.8-31 hms_0.5.3 grid_3.6.3
[118] tidyr_1.0.2 rmarkdown_2.1 git2r_0.26.1
[121] ggforce_0.3.1 Biobase_2.46.0
Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.