+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
++Stat: Import data (phyloseq_import_data.py +v5.1.0) +
+## Import packages
+library(phyloseq)
+library(ggplot2)
+library(ape)
+
+## Settin variables
+ ## The ASV abundance matrix with taxonomy annotation file (biom format)
+ # biomfile <- ""
+
+ ## The sample metadata file(TSV format)
+ # samplefile <- ""
+
+ ## (optional) the ASV tree file (nwk format). Write "None" if you do not have any tree
+ # treefile <- ""
+
+ ## The ordered taxonomic levels stored in BIOM. Each level is separated by one space.
+ ## default : "Kingdom Phylum Class Order Family Genus Species"
+ # ranks <- ""
+
+ ## Do you want to normalise your data ? "True" or "False"
+ # normalisation <- ""
+
+## Create input and parameters dataframe
+ # params <- data.frame( "biomfile" = biomfile, "samplefile" = samplefile, "tree" = tree, "ranks" = ranks, "normalisation" = normalisation)
+
+
+## Import data
+biomfile <- params$biomfile
+data <- import_biom(biomfile)
+sampledata <- read.csv(params$samplefile, sep = "\t", row.names = 1, check.names = FALSE)
+
+# if taxonomy starts with k__ it means that its Greengenes like format
+# import need to be done using parse_taxonomy_greengenes function
+# in this case user taxonomic rank names are ignored
+tax <- tax_table(data)[[1]]
+if ((gregexpr('k__', tax))[[1]][1]>0) {
+ cat("Warning : Taxonomic affiliations come from Greengenes database, user specified ranks names are ignored.")
+ data <- import_biom(biomfile, parseFunction = parse_taxonomy_greengenes)
+} else {
+## else, custumize rank name with the user specified ranks variable
+ new_rank <- as.list(strsplit(params$ranks, " ")[[1]])
+ colnames(tax_table(data)) <- new_rank
+}Warning : Taxonomic affiliations come from Greengenes database, user specified ranks names are ignored.## add sample name to metadata, as SampleID variable
+sampledata$SampleID <- rownames(sampledata)
+sample_data(data) <- sampledata
+
+## add tree metadata if available
+if (params$treefile != "None"){
+ treefile <- read.tree(params$treefile)
+ phy_tree(data) <- treefile
+}
+
+## change de sample metadata order as in input samplefile
+for ( variable in sample_variables(data)){
+ variable.order = as.vector(unique(sampledata[,variable]))
+ sample_data(data)[,variable] <- factor(get_variable(data, variable),levels=variable.order)
+}
+
+## remove empty samples
+empty_samples <- sample_names(data)[which(sample_sums(data)==0)]
+sample_to_keep <- sample_names(data)[which(sample_sums(data)>0)]
+data <- prune_samples(sample_to_keep, data)
+
+empty_taxa <- taxa_names(data)[which(taxa_sums(data)==0)]
+taxa_to_keep <- taxa_names(data)[which(taxa_sums(data)>0)]
+data <- prune_taxa(taxa_to_keep, data)
+
+## abundance normalisation
+if(params$normalisation){ data <- rarefy_even_depth(data, rngseed = 1121983)}
+
+## save phyloseq object in Rdata file
+save(data, file=params$outputRdata)
+
+
+
+
+
+
+
+
+
+
+Summary
+ + + +dataphyloseq-class experiment-level object
+otu_table() OTU Table: [ 507 taxa and 64 samples ]
+sample_data() Sample Data: [ 64 samples by 4 sample variables ]
+tax_table() Taxonomy Table: [ 507 taxa by 7 taxonomic ranks ]
+phy_tree() Phylogenetic Tree: [ 507 tips and 506 internal nodes ]if(length(empty_samples) > 0) {cat(paste('Remove empty samples: ', paste(empty_samples, collapse=",")))}
+if(length(empty_taxa) > 0) {cat(paste('Remove empty taxa: ', paste(empty_taxa, collapse=",")))}Remove empty taxa: otu_01781if(params$normalisation){cat(paste('Number of sequences in each sample after normalisation: ', head(sample_sums(data))[[1]]))}
+
+Ranks Names
+ + + +cat(paste('Rank names : ',paste(rank_names(data),collapse=', ')))Rank names : Kingdom, Phylum, Class, Order, Family, Genus, Species
+
+Sample metadata
+ + + +variables <- sample_variables(data)
+cat(paste('Sample variables: ', paste(variables, collapse=', ' )))Sample variables: EnvType, Description, FoodType, SampleIDfor (var in variables){
+ cat(paste(var,': ',paste(levels(factor(get_variable(data, varName = var))),collapse=', '), '\n\n'))
+}EnvType : BoeufHache, VeauHache, DesLardons, MerguezVolaille, SaumonFume, FiletSaumon, FiletCabillaud, Crevette
+
+Description : LOT1, LOT3, LOT4, LOT5, LOT6, LOT7, LOT8, LOT10, LOT2, LOT9
+
+FoodType : Meat, Seafood
+
+SampleID : BHT0.LOT01, BHT0.LOT03, BHT0.LOT04, BHT0.LOT05, BHT0.LOT06, BHT0.LOT07, BHT0.LOT08, BHT0.LOT10, VHT0.LOT01, VHT0.LOT02, VHT0.LOT03, VHT0.LOT04, VHT0.LOT06, VHT0.LOT07, VHT0.LOT08, VHT0.LOT10, DLT0.LOT01, DLT0.LOT03, DLT0.LOT04, DLT0.LOT05, DLT0.LOT06, DLT0.LOT07, DLT0.LOT08, DLT0.LOT10, MVT0.LOT01, MVT0.LOT03, MVT0.LOT05, MVT0.LOT06, MVT0.LOT07, MVT0.LOT08, MVT0.LOT09, MVT0.LOT10, SFT0.LOT01, SFT0.LOT02, SFT0.LOT03, SFT0.LOT04, SFT0.LOT05, SFT0.LOT06, SFT0.LOT07, SFT0.LOT08, FST0.LOT01, FST0.LOT02, FST0.LOT03, FST0.LOT05, FST0.LOT06, FST0.LOT07, FST0.LOT08, FST0.LOT10, FCT0.LOT01, FCT0.LOT02, FCT0.LOT03, FCT0.LOT05, FCT0.LOT06, FCT0.LOT07, FCT0.LOT08, FCT0.LOT10, CDT0.LOT02, CDT0.LOT04, CDT0.LOT05, CDT0.LOT06, CDT0.LOT07, CDT0.LOT08, CDT0.LOT09, CDT0.LOT10
+
+Plot tree
+ + + +if(params$treefile!="None"){
+ p <- plot_tree(data, color=rank_names(data)[2]) +
+ ggtitle(paste("Phylogenetic tree colored by", rank_names(data)[2])) +
+ theme(plot.title = element_text(hjust = 0.5))
+ plot(p)
+}
if(params$treefile=="None"){
+ cat("There is no phylogenetic tree in the object you have provided.")
+}
+
+Reproducibility token
+ + + +sessioninfo::session_info()─ Session info ───────────────────────────────────────────────────────────────
+ setting value
+ version R version 4.1.2 (2021-11-01)
+ os Ubuntu 24.04.2 LTS
+ system x86_64, linux-gnu
+ ui X11
+ language fr_FR:en
+ collate en_US.utf8
+ ctype en_US.utf8
+ tz Europe/Paris
+ date 2026-01-14
+ pandoc 2.19.2 @ /home/maria/miniforge3/envs/frogs@5.1.0/bin/ (via rmarkdown)
+
+─ Packages ───────────────────────────────────────────────────────────────────
+ package * version date (UTC) lib source
+ ade4 1.7-22 2023-02-06 [1] CRAN (R 4.1.3)
+ ape * 5.7-1 2023-03-13 [1] CRAN (R 4.1.3)
+ Biobase 2.54.0 2021-10-26 [1] Bioconductor
+ BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor
+ biomformat 1.22.0 2021-10-26 [1] Bioconductor
+ Biostrings 2.62.0 2021-10-26 [1] Bioconductor
+ bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.3)
+ bslib 0.5.0 2023-06-09 [1] CRAN (R 4.1.3)
+ cachem 1.0.8 2023-05-01 [1] CRAN (R 4.1.3)
+ cli 3.6.1 2023-03-23 [1] CRAN (R 4.1.3)
+ cluster 2.1.4 2022-08-22 [1] CRAN (R 4.1.3)
+ codetools 0.2-19 2023-02-01 [1] CRAN (R 4.1.3)
+ colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.1.3)
+ crayon 1.5.2 2022-09-29 [1] CRAN (R 4.1.3)
+ data.table 1.14.8 2023-02-17 [1] CRAN (R 4.1.3)
+ digest 0.6.31 2022-12-11 [1] CRAN (R 4.1.3)
+ dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.1.3)
+ evaluate 0.21 2023-05-05 [1] CRAN (R 4.1.3)
+ fansi 1.0.4 2023-01-22 [1] CRAN (R 4.1.3)
+ farver 2.1.1 2022-07-06 [1] CRAN (R 4.1.3)
+ fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.1.3)
+ foreach 1.5.2 2022-02-02 [1] CRAN (R 4.1.3)
+ generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.3)
+ GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor
+ GenomeInfoDbData 1.2.7 2026-01-14 [1] Bioconductor
+ ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.1.3)
+ glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
+ gtable 0.3.3 2023-03-21 [1] CRAN (R 4.1.3)
+ highr 0.10 2022-12-22 [1] CRAN (R 4.1.3)
+ htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.1.3)
+ igraph 1.3.5 2022-09-22 [1] CRAN (R 4.1.3)
+ IRanges 2.28.0 2021-10-26 [1] Bioconductor
+ iterators 1.0.14 2022-02-05 [1] CRAN (R 4.1.3)
+ jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.3)
+ jsonlite 1.8.5 2023-06-05 [1] CRAN (R 4.1.3)
+ knitr 1.43 2023-05-25 [1] CRAN (R 4.1.3)
+ labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.3)
+ lattice 0.21-8 2023-04-05 [1] CRAN (R 4.1.3)
+ lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.3)
+ magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
+ MASS 7.3-58.3 2023-03-07 [1] CRAN (R 4.1.3)
+ Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.1.3)
+ mgcv 1.8-42 2023-03-02 [1] CRAN (R 4.1.3)
+ multtest 2.50.0 2021-10-26 [1] Bioconductor
+ munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.3)
+ nlme 3.1-162 2023-01-31 [1] CRAN (R 4.1.3)
+ permute 0.9-7 2022-01-27 [1] CRAN (R 4.1.3)
+ phyloseq * 1.38.0 2021-10-26 [1] Bioconductor
+ pillar 1.9.0 2023-03-22 [1] CRAN (R 4.1.3)
+ pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.3)
+ plyr 1.8.8 2022-11-11 [1] CRAN (R 4.1.3)
+ R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.3)
+ Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.1.3)
+ RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.1.3)
+ reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.3)
+ rhdf5 2.38.1 2022-03-10 [1] Bioconductor
+ rhdf5filters 1.6.0 2021-10-26 [1] Bioconductor
+ Rhdf5lib 1.16.0 2021-10-26 [1] Bioconductor
+ rlang 1.1.1 2023-04-28 [1] CRAN (R 4.1.3)
+ rmarkdown 2.22 2023-06-01 [1] CRAN (R 4.1.3)
+ rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.1.3)
+ S4Vectors 0.32.4 2022-03-24 [1] Bioconductor
+ sass 0.4.6 2023-05-03 [1] CRAN (R 4.1.3)
+ scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.3)
+ sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.3)
+ stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.1)
+ stringr 1.5.0 2022-12-02 [1] CRAN (R 4.1.3)
+ survival 3.5-5 2023-03-12 [1] CRAN (R 4.1.3)
+ tibble 3.2.1 2023-03-20 [1] CRAN (R 4.1.3)
+ tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.1.3)
+ utf8 1.2.3 2023-01-31 [1] CRAN (R 4.1.3)
+ vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.1.3)
+ vegan 2.6-4 2022-10-11 [1] CRAN (R 4.1.3)
+ withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.3)
+ xfun 0.39 2023-04-20 [1] CRAN (R 4.1.3)
+ XVector 0.34.0 2021-10-26 [1] Bioconductor
+ yaml 2.3.7 2023-01-23 [1] CRAN (R 4.1.3)
+ zlibbioc 1.40.0 2021-10-26 [1] Bioconductor
+
+ [1] /home/maria/miniforge3/envs/frogs@5.1.0/lib/R/library
+
+──────────────────────────────────────────────────────────────────────────────---
copyright: "Copyright (C) 2025 INRAE"
license: "GNU General Public License"
output: 
  html_notebook:
    code_folding: hide
params:
  # Path ASV abundance biom file
  biomfile: 
    value: x
  # Path to sample metadata TSV file
  samplefile:
    value: x
  # (optional) Path to ASVs tree NWK file
  treefile:
    value: x
  # (optional) normalisation string option : TRUE or FALSE
  normalisation:
    value: x
  # Path to phyloseq object store in Rdata file
  outputRdata:
    value: x
  # List of taxonomic ranks names
  ranks : 
    value: x
  # Path to the phyloseq-extend R functions : https://github.com/mahendra-mariadassou/phyloseq-extended, typically stored in FROGS/lib/external-lib
  libdir:
    value: x
  version:
    value: x
  tool:
    value: x
---

<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<meta name="author" content="Ta Thi Ngan - SIGENAE/GABI & Maria Bernard - SIGENAE/GABI" />
<meta name="version" content="5.1.0" />
<meta name="copyright" content="Copyright (C) 2025 INRAE" />

```{r, echo=FALSE, results="asis"}
CURRENT_DIR <- knitr::opts_knit$get("output.dir")
if (is.null(CURRENT_DIR)) {
  CURRENT_DIR <- getwd()
}
THEME_DIR <- normalizePath(
  file.path(dirname(CURRENT_DIR), "static"),
  winslash = "/",
  mustWork = FALSE
)

js_theme_file <- normalizePath(
  file.path(THEME_DIR, "js", "theme.js"),
  winslash = "/",
  mustWork = FALSE
)

lines <- readLines(js_theme_file, warn = FALSE)

sep <- which(grepl("^//##", trimws(lines)))

if (length(sep) < 2) {
  stop("Tag not found in theme.js: '//##'")
}

js_code <- lines[(sep[1] + 1):(sep[2] - 1)]

cat("<script>\n")
cat(js_code, sep = "\n")
cat("\n</script>")
```

<div style="display:flex; align-items:center; gap:15px; margin-bottom:20px;">
  <img id="logo" src="data:image/png;base64," alt="FROGS logo" style="height:180px;">
  <h1 style="margin:0;">Stat: Import data <i><span class="text-accent">(`r params$tool` v`r params$version`)</span></i></h1>
</div>

<script>

$(function () {
  update_logo(CURRENT_THEME);
});


</script>

<style type="text/css">
:root {
			--frogsColor: #03A5A8; 
			--frogsColorHover: hsl(from var(--frogsColor) h calc(s + 4) calc(l - 3) / 1);
			--frogsPreColor: hsl(from var(--frogsColor) h s l / 0.1);
		}
.text-accent {
  color: #595c5f;
}
.main-container{
	max-width: 75% !important;
}
h1{
	color: var(--frogsColor);
}
h2{
	color: var(--frogsColor);
}
a {
	color: var(--frogsColor);
}
a:hover{
	color: var(--frogsColorHover);
}
.nav-pills > li.active > a, .nav-pills > li.active > a:focus{
	color: #fff;
	background-color: var(--frogsColor);
	border-color: #dee2e6 #dee2e6 #fff;
}
.nav-pills > li.active > a:hover {
	background-color: var(--frogsColorHover);
}
.button {
    background-color: var(--frogsColor) ;
    border          : none;
    color           : white;
    padding         : 5px 10px;
    text-align      : center;
    text-decoration : none;
    display         : inline-block;
    font-size       : 12px;
    margin          : 4px 2px;
    cursor          : pointer;
    border-radius   : 8px;
}
h4 { 
    display      : block;
    font-size    : 1em;
    margin-top   : 1.33em;
    margin-bottom: 1.33em;
    margin-left  : 0;
    margin-right : 0;
    font-weight  : bold;
    color        : var(--frogsColor);
}
code.r{ /* Code block */
  font-size: 11px;
}
pre{
  font-size: 11px ;
  background-color: var(--frogsPreColor) !important;
}
#themechoice{
  border-radius: 0.25em;
  background-color: white;
  border: 1px solid #dee2e6;
  font-weight: 400;
  line-height: 1.5;
  padding: .375rem 2.25rem .375rem .75rem;
}
</style>
 
```{r package_import, message=FALSE, warning=FALSE}

## Import packages
library(phyloseq)
library(ggplot2)
library(ape)

## Settin variables
  ## The ASV abundance matrix with taxonomy annotation file (biom format)
  # biomfile <- ""

  ## The sample metadata file(TSV format)
  # samplefile <- ""

  ## (optional) the ASV tree file (nwk format). Write "None" if you do not have any tree
  # treefile <- ""

  ## The ordered taxonomic levels stored in BIOM. Each level is separated by one space.
  ## default : "Kingdom Phylum Class Order Family Genus Species"
  # ranks <- ""

  ## Do you want to normalise your data ? "True" or "False"
  # normalisation <- ""

## Create input and parameters dataframe
  # params <- data.frame( "biomfile" = biomfile, "samplefile" = samplefile, "tree" = tree, "ranks" = ranks, "normalisation" = normalisation)


## Import data
biomfile <- params$biomfile
data     <- import_biom(biomfile)
sampledata <- read.csv(params$samplefile, sep = "\t", row.names = 1, check.names = FALSE)

# if taxonomy starts with k__ it means that its Greengenes like format
# import need to be done using parse_taxonomy_greengenes function
# in this case user taxonomic rank names are ignored
tax      <- tax_table(data)[[1]]
if ((gregexpr('k__', tax))[[1]][1]>0) { 
  cat("Warning : Taxonomic affiliations come from Greengenes database, user specified ranks names are ignored.")
  data <- import_biom(biomfile, parseFunction = parse_taxonomy_greengenes)
} else {
## else, custumize rank name with the user specified ranks variable
  new_rank <- as.list(strsplit(params$ranks, " ")[[1]])
  colnames(tax_table(data)) <- new_rank
}

## add sample name to metadata, as SampleID variable
sampledata$SampleID <- rownames(sampledata)
sample_data(data) <- sampledata

## add tree metadata if available
if (params$treefile != "None"){
  treefile <- read.tree(params$treefile)
  phy_tree(data) <- treefile
}

## change de sample metadata order as in input samplefile
for ( variable in sample_variables(data)){
  variable.order = as.vector(unique(sampledata[,variable]))
  sample_data(data)[,variable] <- factor(get_variable(data, variable),levels=variable.order)
}

## remove empty samples
empty_samples <- sample_names(data)[which(sample_sums(data)==0)]
sample_to_keep <- sample_names(data)[which(sample_sums(data)>0)]
data <- prune_samples(sample_to_keep, data)

empty_taxa <- taxa_names(data)[which(taxa_sums(data)==0)]
taxa_to_keep <- taxa_names(data)[which(taxa_sums(data)>0)]
data <- prune_taxa(taxa_to_keep, data)

## abundance normalisation
if(params$normalisation){ data <- rarefy_even_depth(data, rngseed = 1121983)}

## save phyloseq object in Rdata file
save(data, file=params$outputRdata)
```

# {.tabset .tabset-fade .tabset-pills}

```{=html}
<div class="row">
  <div style="float:right">
  <select id="themechoice"
          class="form-select form-select-sm"
          style="width: auto;"
          onchange="update_theme_Rmd(this.value)"
          aria-label="Switch theme">
    <option selected disabled value="">Switch theme</option>
    <option disabled value="DefaultTheme">Default</option>
    <option value="CoralTheme">Coral</option>
    <option value="GoldTheme">Gold</option>
    <option value="SteelTheme">Steel</option>
  </select>
  </div>
</div>
```

## Summary
```{r summary}
data
if(length(empty_samples) > 0) {cat(paste('Remove empty samples: ', paste(empty_samples, collapse=",")))}
if(length(empty_taxa) > 0) {cat(paste('Remove empty taxa: ', paste(empty_taxa, collapse=",")))}
if(params$normalisation){cat(paste('Number of sequences in each sample after normalisation: ', head(sample_sums(data))[[1]]))}
```

## Ranks Names
```{r ranks}
cat(paste('Rank names : ',paste(rank_names(data),collapse=', ')))
```

## Sample metadata
```{r sample}
variables <- sample_variables(data)
cat(paste('Sample variables: ', paste(variables, collapse=', ' )))

for (var in variables){
  cat(paste(var,': ',paste(levels(factor(get_variable(data, varName = var))),collapse=', '), '\n\n'))
}
```

## Plot tree
```{r tree, fig.width=10, fig.height=8}

if(params$treefile!="None"){
  p <- plot_tree(data, color=rank_names(data)[2]) + 
          ggtitle(paste("Phylogenetic tree colored by", rank_names(data)[2])) + 
          theme(plot.title = element_text(hjust = 0.5))
  plot(p)
}

if(params$treefile=="None"){
  cat("There is no phylogenetic tree in the object you have provided.")
}
```

## Reproducibility token

```{r session, echo=TRUE, eval=TRUE}
sessioninfo::session_info()
```
+
+
+
+
