real_samples.Rmd 10.9 KB
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---
title: "Real samples analysis"
description: |
  METABARFOOD project.
author: Olivier Rué
date: '`r Sys.Date()`'
output:
  html_document:
    self_contained: false
    number_sections: FALSE
    code_folding: "show"
    toc: true
    toc_depth: 5
    toc_float: true
---

<link href="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/7.0.10/jquery.nouislider.min.css" rel="stylesheet"/>
<script src="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/7.0.10/jquery.nouislider.min.js"></script>
<link href="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.0/css/selectize.bootstrap3.min.css" rel="stylesheet" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.0/js/standalone/selectize.min.js"></script>

```{r setup, include=FALSE}
knitr::opts_chunk$set(eval=FALSE, echo =T, cache = FALSE, message = FALSE, warning = FALSE, cache.lazy = FALSE, fig.height = 3.5, fig.width = 10.5)
```

```{r, setup1, echo=FALSE, message = FALSE, warning = FALSE, eval=TRUE}
library(DT)
library(ggpubr)
library(kableExtra)
library(seqinr)
library(gridExtra)
library(phyloseq)
library(phyloseq.extended)
library(tidyverse)
library(plotly)
library(qiime2R)
library(tidyverse)
library(ComplexHeatmap)
library(phyloseqCompanion)
library(circlize)
```


```{r datatable global options, echo=FALSE, eval=TRUE}
options(DT.options = list(pageLength = 10,
                         scrollX = TRUE,
                         language = list(search = 'Filter:'),
                         dom = 'Bfrtip',
                         buttons = c('copy', 'csv', 'excel', 'pdf', 'print')))
```

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# MEAT
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```{bash, eval=F}
# Genologin
cd /work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/scripts
sh dada2_frogs.sh
```

```{bash, eval=F}
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#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.biom MEAT/ITS1.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.biom MEAT/ITS2.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.biom MEAT/D1D2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.biom MEAT/RPB2.biom

#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/frogs.tsv MEAT/ITS1.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/frogs.tsv MEAT/ITS2.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/frogs.tsv MEAT/D1D2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/frogs.tsv MEAT/RPB2.tsv

#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS1/multiaff.tsv MEAT/ITS1_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/ITS2/multiaff.tsv MEAT/ITS2_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/D1D2/multiaff.tsv MEAT/D1D2_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/multiaff.tsv MEAT/RPB2_multiaff.tsv
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```

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## Preparation of final BIOM files {.tabset}

### ITS1

### ITS2

### D1D2

### RPB2

## Analysis

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```{r, eval=F}
if (!file.exists("REAL/ITS1.rds")) {
  biomfile <- "REAL/ITS1.biom"
  physeq_its1 <- import_frogs(biomfile, taxMethod = "blast")
  metadata <- read.table("REAL/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
  sample_data(physeq_its1) <- metadata
  sample_data(physeq_its1)$Marker <- "ITS1"
  saveRDS(physeq_its1,"REAL/ITS1.rds")
} else {
  physeq_its1 <- readRDS("REAL/ITS1.rds")
}

if (!file.exists("REAL/ITS2.rds")) {
  biomfile <- "REAL/ITS2.biom"
  physeq_its2 <- import_frogs(biomfile, taxMethod = "blast")
  metadata <- read.table("REAL/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
  sample_data(physeq_its2) <- metadata
  sample_data(physeq_its2)$Marker <- "ITS2"
  saveRDS(physeq_its2,"REAL/ITS2.rds")
} else {
  physeq_its2 <- readRDS("REAL/ITS2.rds")
}

if (!file.exists("REAL/D1D2.rds")) {
  biomfile <- "REAL/D1D2.biom"
  physeq_d1d2 <- import_frogs(biomfile, taxMethod = "blast")
  metadata <- read.table("REAL/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
  sample_data(physeq_d1d2) <- metadata
  sample_data(physeq_d1d2)$Marker <- "D1D2"
  saveRDS(physeq_d1d2,"REAL/D1D2.rds")
} else {
  physeq_d1d2 <- readRDS("REAL/D1D2.rds")
}

if (!file.exists("REAL/RPB2.rds")) {
  biomfile <- "REAL/RPB2.biom"
  physeq_rpb2 <- import_frogs(biomfile, taxMethod = "blast")
  metadata <- read.table("REAL/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
  sample_data(physeq_rpb2) <- metadata
  sample_data(physeq_rpb2)$Marker <- "RPB2"
  saveRDS(physeq_rpb2,"REAL/RPB2.rds")
} else {
  physeq_rpb2 <- readRDS("REAL/RPB2.rds")
}
```


```{r, eval=T}
create_frogs_object <- function(path, marker, type, file, multifile){
  biom <- file.path(path,file)
  physeq <- import_frogs(biom, taxMethod = "blast")
  metadata_file <- file.path(path,"metadata.tsv")
  metadata <- read.table(metadata_file, row.names=1, header=TRUE, sep="\t", stringsAsFactors = FALSE)

  sample_data(physeq) <- metadata
  multiaff_file <- file.path(path,multifile)
  physeq <- update_frogs_physeq_with_multi(physeq, multiaff_file)
  #physeq  = transform_sample_counts(physeq, function(x) x / sum(x) )
  sample_names(physeq) <- glue::glue(paste("{sample_names(physeq)}","DF",marker, sep="_"))
  sample_data(physeq)$method <- "DADA2_FROGS"
  sample_data(physeq)$Type <- type
  sample_data(physeq)$Marker <- marker
  physeq_aglom <- phyloseq.extended::fast_tax_glom(physeq, taxrank = "Species")
  #physeq_aglom <- prune_taxa(tax_table(physeq_aglom)[,7] %in% references, physeq_aglom)
  taxa_names(physeq_aglom) <- cbind(tax_table(physeq_aglom)[,7])
  return(physeq_aglom)
}

update_frogs_physeq_with_multi <- function(physeq, multiaff_file){

  infos <- readr::read_tsv(file = multiaff_file) %>%
    as_tibble() %>%
    distinct(`#observation_name`, .keep_all = T) %>%
    select(`#observation_name`, blast_taxonomy) %>%
    separate(blast_taxonomy, ";(?=[\\S])", into = c("Kingdom","Phylum","Class","Order","Family","Genus","Species")) %>%
    #mutate(across(Kingdom:Species, ~ stringr::str_remove(.x, ".:"))) %>%
    tibble::column_to_rownames(var = "#observation_name") %>%
    as("matrix")

  good <- tax_table(subset_taxa(physeq, Species != "Multi-affiliation" & Genus != "Multi-affiliation" & Family != "Multi-affiliation" & Order != "Multi-affiliation" & Class != "Multi-affiliation" & Phylum != "Multi-affiliation" & Kingdom != "Multi-affiliation" )) %>% as("matrix")
  #na <- tax_table(subset_taxa(physeq, is.na(Species))) %>%  as("matrix")
  all_infos <- unique(rbind(infos,good))#,na) # case where two species are identical but are multi-affiliated
  tax_table(physeq) <- all_infos

  return(physeq)
}


keep_only_interest_species <- function(physeq, true_species){
   tax_tab <- tax_table(physeq) %>% as("matrix")
   tax_tab <- cbind(tax_tab[ , 1:7],
                    Status = ifelse(tax_tab[ , "Species"] %in% true_species, "true species", "artefact"))
   tax_table(physeq) <- tax_tab
   return(physeq)
}
```


```{r, eval=T}
rpb2 <- create_frogs_object("REAL","RPB2", "DNA", "RPB2.biom", "RPB2_multiaff.tsv")
tax_table(rpb2)[, colnames(tax_table(rpb2))] <- gsub(tax_table(rpb2)[, colnames(tax_table(rpb2))],     pattern = "[a-z]:", replacement = "")
d1d2 <- create_frogs_object("REAL","D1D2", "DNA", "D1D2.biom", "D1D2_multiaff.tsv")
tax_table(d1d2)[, colnames(tax_table(d1d2))] <- gsub(tax_table(d1d2)[, colnames(tax_table(d1d2))],     pattern = "[a-z]:", replacement = "")
its1 <- create_frogs_object("REAL","ITS1", "DNA", "ITS1.biom", "ITS1_multiaff.tsv")
its2 <- create_frogs_object("REAL","ITS2", "DNA", "ITS2.biom", "ITS2_multiaff.tsv")

all <- merge_phyloseq(its1, its2, d1d2, rpb2)

sample_data(all)$Marker <- factor(sample_data(all)$Marker, levels=c("ITS1","ITS2","D1D2","RPB2"))
Method <- get_variable(all, "method")

saveRDS(all, "REAL/real_all.rds")



```


```{r, eval=T}
p <- plot_bar(all)
p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
```

```{r, eval=T}
p <- plot_composition(physeq = all, taxaRank1 = "Kingdom", taxaSet1 = "Fungi", taxaRank2 = "Genus", numberOfTaxa = 22, x = "Sample")
p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
```

```{r, eval=T}
p <- plot_composition(physeq = all, taxaRank1 = "Kingdom", taxaSet1 = "Fungi", taxaRank2 = "Species", numberOfTaxa = 22, x = "Sample")
p + facet_grid(". ~ Marker", scales = "free_x", space = "free")
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```

# CHEESE

```{bash, eval=F}
# Genologin
cd /work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/scripts
sh dada2_frogs.sh
```

```{bash, eval=F}
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/frogs.biom CHEESE/ITS1.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/frogs.biom CHEESE/ITS2.biom
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/frogs.biom CHEESE/D1D2.biom
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/frogs.biom CHEESE/RPB2.biom

#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/frogs.tsv CHEESE/ITS1.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/frogs.tsv CHEESE/ITS2.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/frogs.tsv CHEESE/D1D2.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/frogs.tsv CHEESE/RPB2.tsv

#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS1/multiaff.tsv CHEESE/ITS1_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/ITS2/multiaff.tsv CHEESE/ITS2_multiaff.tsv
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/D1D2/multiaff.tsv CHEESE/D1D2_multiaff.tsv
scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/multiaff.tsv CHEESE/RPB2_multiaff.tsv
```


## Preparation of final BIOM files {.tabset}

### ITS1

### ITS2

### D1D2

### RPB2

## Analysis