Last updated: 2020-05-16
Checks: 6 1
Knit directory: SolFaMi_bioinfo/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | bf17f72 | adrientaudiere | 2020-05-16 | workflowr::wflow_publish(“analysis/Bioinfo.Rmd”) |
| Rmd | e6e7518 | adrientaudiere | 2020-05-16 | Fix the wflow_publish report in drake plan |
| html | e6e7518 | adrientaudiere | 2020-05-16 | Fix the wflow_publish report in drake plan |
| 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 |
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| Rmd | 2a1f393 | adrientaudiere | 2020-04-28 | workflowr::wflow_publish(all = T) |
| Rmd | b5a3cac | adrientaudiere | 2020-04-28 | Update package |
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| Rmd | 81e0125 | adrientaudiere | 2020-04-28 | try publish 2 |
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| 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")Le chargement a nécessité le package : conflictedLe chargement a nécessité le package : ggplot2Le chargement a nécessité le package : gridExtraLe chargement a nécessité le package : BiocManagerBioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for helpBioconductor version '3.10' is out-of-date; the current release version '3.11'
is available with R version '4.0'; see https://bioconductor.org/installLe chargement a nécessité le package : devtoolsLe chargement a nécessité le package : usethis
Attachement du package : 'devtools'The following object is masked from 'package:BiocManager':
installLe chargement a nécessité le package : drake
Attachement du package : 'drake'The following object is masked from 'package:devtools':
checkLe chargement a nécessité le package : RcppLe chargement a nécessité le package : readxlLe chargement a nécessité le package : forcatsLe chargement a nécessité le package : visNetworkLe chargement a nécessité le package : lubridate
Attachement du package : 'lubridate'The following objects are masked from 'package:base':
date, intersect, setdiff, unionLe chargement a nécessité le package : herehere() starts at /home/adrien/Bureau/Analyse_Solfami/SolFaMi_bioinfoLe chargement a nécessité le package : networkD3Le chargement a nécessité le package : ggraphLe chargement a nécessité le package : qsqs v0.21.2. See ChangeLog for update info.Le chargement a nécessité le package : stylerLe chargement a nécessité le package : dplyr
Attachement du package : 'dplyr'The following objects are masked from 'package:lubridate':
intersect, setdiff, unionThe following object is masked from 'package:gridExtra':
combineThe following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionLe chargement a nécessité le package : formattableLe chargement a nécessité le package : pbapplyLe chargement a nécessité le package : dada2Le chargement a nécessité le package : phyloseqLe chargement a nécessité le package : DECIPHERLe chargement a nécessité le package : BiostringsLe chargement a nécessité le package : BiocGenericsLe chargement a nécessité le package : parallel
Attachement du package : 'BiocGenerics'The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLBThe following object is masked from 'package:formattable':
normalizeThe following objects are masked from 'package:dplyr':
combine, intersect, setdiff, unionThe following objects are masked from 'package:lubridate':
intersect, setdiff, unionThe following object is masked from 'package:gridExtra':
combineThe following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.minLe chargement a nécessité le package : S4VectorsLe chargement a nécessité le package : stats4
Attachement du package : 'S4Vectors'The following objects are masked from 'package:dplyr':
first, renameThe following objects are masked from 'package:lubridate':
second, second<-The following object is masked from 'package:drake':
expandThe following object is masked from 'package:base':
expand.gridLe chargement a nécessité le package : IRanges
Attachement du package : 'IRanges'The following object is masked from 'package:phyloseq':
distanceThe following objects are masked from 'package:dplyr':
collapse, desc, sliceThe following object is masked from 'package:lubridate':
%within%Le chargement a nécessité le package : XVector
Attachement du package : 'Biostrings'The following object is masked from 'package:base':
strsplitLe chargement a nécessité le package : RSQLiteLe chargement a nécessité le package : speedyseq
Attachement du package : 'speedyseq'The following objects are masked from 'package:phyloseq':
plot_bar, plot_heatmap, plot_tree, psmelt, tax_glom, tip_glom* The lockfile is already up to date.# r_make() # need to run r_make if you change the planvis_drake_graph(plan, envir = drake_envir)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: phyloseqtrack_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 |
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
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils
[8] methods base
other attached packages:
[1] tidyselect_1.0.0 speedyseq_0.1.2.9004 DECIPHER_2.14.0
[4] RSQLite_2.2.0 Biostrings_2.54.0 XVector_0.26.0
[7] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
[10] phyloseq_1.30.0 dada2_1.14.1 pbapply_1.4-2
[13] formattable_0.2.0.1 dplyr_0.8.5 styler_1.3.2
[16] qs_0.21.2 ggraph_2.0.2 networkD3_0.4
[19] here_0.1 lubridate_1.7.8 visNetwork_2.0.9
[22] forcats_0.5.0 readxl_1.3.1 Rcpp_1.0.4.6
[25] drake_7.12.0 devtools_2.3.0 usethis_1.6.0
[28] BiocManager_1.30.10 gridExtra_2.3 ggplot2_3.3.0
[31] conflicted_1.0.4 knitr_1.28 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] backports_1.1.6 plyr_1.8.6
[3] igraph_1.2.5 splines_3.6.3
[5] storr_1.2.1 RApiSerialize_0.1.0
[7] BiocParallel_1.20.1 GenomeInfoDb_1.22.1
[9] digest_0.6.25 foreach_1.5.0
[11] htmltools_0.4.0 viridis_0.5.1
[13] fansi_0.4.1 magrittr_1.5
[15] memoise_1.1.0 base64url_1.4
[17] cluster_2.1.0 remotes_2.1.1
[19] graphlayouts_0.7.0 RcppParallel_5.0.0
[21] matrixStats_0.56.0 prettyunits_1.1.1
[23] jpeg_0.1-8.1 colorspace_1.4-1
[25] blob_1.2.1 ggrepel_0.8.2
[27] xfun_0.13 callr_3.4.3
[29] crayon_1.3.4 RCurl_1.98-1.2
[31] jsonlite_1.6.1 survival_3.1-12
[33] iterators_1.0.12 ape_5.3
[35] glue_1.4.0 polyclip_1.10-0
[37] gtable_0.3.0 zlibbioc_1.32.0
[39] DelayedArray_0.12.3 pkgbuild_1.0.7
[41] Rhdf5lib_1.8.0 scales_1.1.0
[43] DBI_1.1.0 viridisLite_0.3.0
[45] progress_1.2.2 bit_1.1-15.2
[47] txtq_0.2.0 htmlwidgets_1.5.1
[49] RColorBrewer_1.1-2 ellipsis_0.3.0
[51] pkgconfig_2.0.3 farver_2.0.3
[53] rlang_0.4.5 reshape2_1.4.4
[55] later_1.0.0 munsell_0.5.0
[57] cellranger_1.1.0 tools_3.6.3
[59] cli_2.0.2 generics_0.0.2
[61] ade4_1.7-15 evaluate_0.14
[63] biomformat_1.14.0 stringr_1.4.0
[65] yaml_2.2.1 bit64_0.9-7
[67] processx_3.4.2 fs_1.4.1
[69] tidygraph_1.1.2 purrr_0.3.4
[71] nlme_3.1-147 whisker_0.4
[73] compiler_3.6.3 filelock_1.0.2
[75] png_0.1-7 testthat_2.3.2
[77] tibble_3.0.1 tweenr_1.0.1
[79] stringi_1.4.6 ps_1.3.2
[81] desc_1.2.0 lattice_0.20-41
[83] Matrix_1.2-18 permute_0.9-5
[85] vegan_2.5-6 multtest_2.42.0
[87] vctrs_0.2.4 pillar_1.4.3
[89] lifecycle_0.2.0 data.table_1.12.8
[91] bitops_1.0-6 httpuv_1.5.2
[93] GenomicRanges_1.38.0 R6_2.4.1
[95] latticeExtra_0.6-29 hwriter_1.3.2
[97] promises_1.1.0 renv_0.9.3
[99] ShortRead_1.44.3 sessioninfo_1.1.1
[101] codetools_0.2-16 MASS_7.3-51.6
[103] assertthat_0.2.1 pkgload_1.0.2
[105] rhdf5_2.30.1 SummarizedExperiment_1.16.1
[107] rprojroot_1.3-2 withr_2.2.0
[109] GenomicAlignments_1.22.1 Rsamtools_2.2.3
[111] GenomeInfoDbData_1.2.2 mgcv_1.8-31
[113] hms_0.5.3 grid_3.6.3
[115] tidyr_1.0.2 rmarkdown_2.1
[117] git2r_0.26.1 ggforce_0.3.1
[119] Biobase_2.46.0