ICD

Accompaniement of Anaïs Brosse in her analyses

closed

collaboration

Authors

Affiliation

Olivier Rué

Migale bioinformatics facility

Christelle Hennequet-Antier

Migale bioinformatics facility

Published

July 5, 2023

Modified

December 19, 2023

Show the code

#library(DT)
library(tidyverse)
#library(kableExtra)
library(phyloseq)
library(phyloseq.extended)
library(data.table)
library(InraeThemes)
library(readr) #read_delim
library(ggplot2)      # graphics
library(microbiome) # for boxplot_alpha function
library(mia) # microbiome analysis with SummarizedExperiment and TreeSummarizedExperiment
library(emmeans) #post hoc tests
library(reactable) #table formatting and styling
library(reactablefmtr) #table formatting and styling
library(openxlsx) #save results to excel sheets
library(metacoder) # differential abundance
library(ggtree) # visualization
library(ggtreeExtra) # visualization

Note

This document is a report of the analyses performed. You will find all the code used to analyze these data. The version of the tools (maybe in code chunks) and their references are indicated, for questions of reproducibility.

Aim of the project

Influence of treatment antibiotics in a murine model of infection with Clostridium difficile (ICD). Injection of C. difficile were performed at J00 and J37.

Différencier les groupes ctrl et traités aux antibiotiques (VAN, MTZ, FDX, R = réinfections multiples), et comparer les cinétiques entre les groupes.
Etudier les cinétiques au sein des traitements (CTRL, VAN, MTZ, FDX, R). Est-ce qu’il y a un retour à J-6 ? Clairance de la bactérie (zéro dans les fécès, attention biofilm et sporulation peuvent encore existés)
Eubiose : comparer J-6, J28, J51.

Partners

Olivier Rué - Migale bioinformatics facility - BioInfomics - INRAE
Christelle Hennequet-Antier - Migale bioinformatics facility - BioInfomics - INRAE
Mahendra Mariadassou - Migale bioinformatics facility - BioInfomics - INRAE
Anaïs Brosse - MICALIS - INRAE

Data management

Important

All data is managed by the migale facility for the duration of the project. Once the project is over, the Migale facility does not keep your data. We will provide you with the raw data and associated metadata that will be deposited on public repositories before the results are used. We can guide you in the submission process. We will then decide which files to keep, knowing that this report will also be provided to you and that the analyses can be replayed if needed.

Diversity Analyses with all samples

Important

Note that the rarefaction was performed on samples from the study including only R and CTRL treatments. Alpha and beta diversities were calculated on this new frogs_rare phyloseq object.

Important

Note that the rarefaction was performed on samples from the study excluding R treatment. Alpha and beta diversities were calculated on this new frogs_rare phyloseq object.

Reports on diversity analyses for each phyloseq object

	Description
	Excel file containing the results of alpha diversity tests for the complete study
	Excel file containing the results of alpha diversity tests for the study including only CTRL and R treatments with rarefaction based on the complete study
	Excel file containing the results of alpha diversity tests on the study excluding R treatment with rarefaction based on the complete study
	Excel file containing the results of alpha diversity tests to evaluate dysbiose on the study excluding R treatment for J-6 J0 and J5 with rarefaction based on the complete study
	Excel file containing the results of alpha diversity tests for the study including only CTRL and R treatments
	Excel file containing the results of alpha diversity tests for the study excluding R treatment
	RDS file to load in Easy16S

Eubiose - Differential Abundance Analysis

Differential abundance analysis (daa) : les états d’eubiose sont-ils équivalents aux jours J-6, J28, J51 ?

Reports on diversity analyses and differential abundance analysis

Eubiose

	Description
	Excel file containing the results of alpha diversity tests for eubiose samples with rarefaction based on the complete study
	Excel file containing the results of differential abundance analysis concerning eubiose contrasts

Without R samples - Differential Abundance Analysis

Differential abundance analysis (daa) : all samples without R.

Reports on diversity analyses and differential abundance analysis

WithoutR_DAA

	Description
	Excel file containing the results of alpha diversity tests for the study without R samples with rarefaction based on the complete study
	Excel file containing the results of differential abundance analysis between consecutive days and eubiose days
	Excel file containing the results of differential abundance analysis between GROUP treatment
	Excel file containing the results of differential abundance analysis between GROUP treatment at D05, D07, D14 days

Reuse

This document will not be accessible without prior agreement of the partners

A work by Migale Bioinformatics Facility
Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, 78350, Jouy-en-Josas, France

--- title: "ICD" search: false navbar: false subtitle: "Accompaniement of Anaïs Brosse in her analyses" author: - name: Olivier Rué orcid: 0000-0003-1689-0557 email: olivier.rue@inrae.fr affiliations: - name: Migale bioinformatics facility adress: Domaine de Vilvert city: Jouy-en-Josas state: France - name: Christelle Hennequet-Antier orcid: 0000-0001-5836-2803 email: christelle.hennequet-antier@inrae.fr affiliations: - name: Migale bioinformatics facility adress: Domaine de Vilvert city: Jouy-en-Josas state: France date: "2023-07-05" date-modified: "2023-12-19" image: "images/preview.jpg" reader-mode: false fig-cap-location: bottom tbl-cap-location: top license: "This document will not be accessible without prior agreement of the partners" format: html: embed-resources: false toc: true code-fold: true code-summary: "Show the code" code-tools: true toc-location: right page-layout: article code-overflow: wrap categories: [closed, collaboration] --- ```{r setup, include=FALSE} knitr::opts_chunk$set(eval=TRUE, echo =TRUE, cache = FALSE, message = FALSE, warning = FALSE, cache.lazy = FALSE, fig.height = 3.5, fig.width = 10) ``` ```{r} #| label: load-packages #library(DT) library(tidyverse) #library(kableExtra) library(phyloseq) library(phyloseq.extended) library(data.table) library(InraeThemes) library(readr) #read_delim library(ggplot2) # graphics library(microbiome) # for boxplot_alpha function library(mia) # microbiome analysis with SummarizedExperiment and TreeSummarizedExperiment library(emmeans) #post hoc tests library(reactable) #table formatting and styling library(reactablefmtr) #table formatting and styling library(openxlsx) #save results to excel sheets library(metacoder) # differential abundance library(ggtree) # visualization library(ggtreeExtra) # visualization ```        {{< include /resources/_includes/_intro_note.qmd >}} # Aim of the project Influence of treatment antibiotics in a murine model of infection with *Clostridium difficile* (ICD). Injection of *C. difficile* were performed at `J00` and `J37`. - Différencier les groupes ctrl et traités aux antibiotiques (VAN, MTZ, FDX, R = réinfections multiples), et comparer les cinétiques entre les groupes. - Etudier les cinétiques au sein des traitements (CTRL, VAN, MTZ, FDX, R). Est-ce qu’il y a un retour à J-6 ? Clairance de la bactérie (zéro dans les fécès, attention biofilm et sporulation peuvent encore existés) - Eubiose : comparer J-6, J28, J51. ## Partners * Olivier Rué - Migale bioinformatics facility - BioInfomics - INRAE * Christelle Hennequet-Antier - Migale bioinformatics facility - BioInfomics - INRAE * Mahendra Mariadassou - Migale bioinformatics facility - BioInfomics - INRAE * Anaïs Brosse - MICALIS - INRAE # Data management {{< include /resources/_includes/_data_management.qmd >}} # Diversity Analyses with all samples ```{r} #| label: diversity_all #| include: false script_name <- paste("1_Diversity_", "All",".qmd", sep='') file.copy(from = file.path("./script",script_name), to = file.path("./html",script_name), overwrite = TRUE) quarto::quarto_render( input = file.path("html",script_name), execute_dir = "./html/", cache_refresh = TRUE, use_freezer = TRUE ) ``` ::: {.callout-important} Note that the rarefaction was performed on samples from the study including only R and CTRL treatments. Alpha and beta diversities were calculated on this new `frogs_rare` phyloseq object. ::: ```{r} #| label: diversity_withR #| include: false experiment <- "withR" #experiment <- "withoutR" script_name <- paste("2_Diversity_subset_", experiment,".qmd", sep='') file.copy(from = file.path("./script", "2_Diversity_subset.qmd"), to = file.path("./html", script_name), overwrite = TRUE) quarto::quarto_render( input = file.path("html", script_name), execute_params = list( my.interest = experiment ), execute_dir = "./html/", cache_refresh = TRUE, use_freezer = TRUE ) ``` ::: {.callout-important} Note that the rarefaction was performed on samples from the study excluding R treatment. Alpha and beta diversities were calculated on this new `frogs_rare` phyloseq object. ::: ```{r} #| label: diversity_withoutR #| include: false #experiment <- "withR" experiment <- "withoutR" script_name <- paste("2_Diversity_subset_", experiment,".qmd", sep='') file.copy(from = file.path("./script", "2_Diversity_subset.qmd"), to = file.path("./html", script_name), overwrite = TRUE) quarto::quarto_render( input = file.path("html", script_name), execute_params = list( my.interest = experiment ), execute_dir = "./html/", cache_refresh = TRUE, use_freezer = TRUE ) ``` Reports on diversity analyses for each phyloseq object * [ALL](./html/1_Diversity_All.html) * [with-R-treatment](./html/2_Diversity_subset_withR.html) * [without-R-treatment](./html/2_Diversity_subset_withoutR.html) |   | Description | |------|------| | {{< downloadthis ./html/comparisons_alpha_diversity.xlsx >}} | Excel file containing the results of alpha diversity tests for the complete study | | {{< downloadthis ./html/comparisons_alpha_diversity_rareAll_withR.xlsx >}} | Excel file containing the results of alpha diversity tests for the study including only CTRL and R treatments with rarefaction based on the complete study | | {{< downloadthis ./html/comparisons_alpha_diversity_rareAll_withoutR.xlsx >}} | Excel file containing the results of alpha diversity tests on the study excluding R treatment with rarefaction based on the complete study | | {{< downloadthis ./html/comparisons_alpha_diversity_rareAll_dysbiose_withoutR.xlsx >}} | Excel file containing the results of alpha diversity tests to evaluate dysbiose on the study excluding R treatment for J-6 J0 and J5 with rarefaction based on the complete study | | {{< downloadthis ./html/comparisons_alpha_diversity_withR.xlsx >}} | Excel file containing the results of alpha diversity tests for the study including only CTRL and R treatments | | {{< downloadthis ./html/comparisons_alpha_diversity_withoutR.xlsx >}} | Excel file containing the results of alpha diversity tests for the study excluding R treatment | | {{< downloadthis ./html/frogs.rds >}} | RDS file to load in [Easy16S](https://shiny.migale.inrae.fr/app/easy16S) | # Eubiose - Differential Abundance Analysis Differential abundance analysis (daa) : les états d’eubiose sont-ils équivalents aux jours J-6, J28, J51 ? ```{r} #| label: eubiose_daa #| include: false script_name <- paste("3_eubiose_anadiff", ".qmd", sep='') file.copy(from = file.path("./script",script_name), to = file.path("./html",script_name), overwrite = TRUE) quarto::quarto_render( input = file.path("html",script_name), execute_dir = "./html/", cache_refresh = TRUE, use_freezer = FALSE ) ``` Reports on diversity analyses and differential abundance analysis * [Eubiose](./html/3_eubiose_anadiff.html) |   | Description | |------|------| | {{< downloadthis ./html/comparisons_alpha_diversity_rareAll_eubiose_withoutR.xlsx >}} | Excel file containing the results of alpha diversity tests for eubiose samples with rarefaction based on the complete study | | {{< downloadthis ./html/daa_deseq2_eubiose_withoutR.xlsx >}} | Excel file containing the results of differential abundance analysis concerning eubiose contrasts | # Without R samples - Differential Abundance Analysis Differential abundance analysis (daa) : all samples without R. ```{r} #| label: withoutR_daa #| include: false script_name <- paste("4_withoutR_anadiff", ".qmd", sep='') file.copy(from = file.path("./script",script_name), to = file.path("./html",script_name), overwrite = TRUE) quarto::quarto_render( input = file.path("html",script_name), execute_dir = "./html/", cache_refresh = TRUE, use_freezer = FALSE ) ``` Reports on diversity analyses and differential abundance analysis * [WithoutR_DAA](./html/4_withoutR_anadiff.html) |   | Description | |------|------| | {{< downloadthis ./html/comparisons_alpha_diversity_rareAll_withoutR.xlsx >}} | Excel file containing the results of alpha diversity tests for the study without R samples with rarefaction based on the complete study | | {{< downloadthis ./html/daa_deseq2_DAY_consec_eubiose_withoutR.xlsx >}} | Excel file containing the results of differential abundance analysis between consecutive days and eubiose days | | {{< downloadthis ./html/daa_deseq2_GROUP_withoutR.xlsx >}} | Excel file containing the results of differential abundance analysis between GROUP treatment | | {{< downloadthis ./html/daa_deseq2_D05_D07_D14_withoutR.xlsx >}} | Excel file containing the results of differential abundance analysis between GROUP treatment at D05, D07, D14 days |