From cc4ddf8d0f73d648cbd8b65bba2848000e148e67 Mon Sep 17 00:00:00 2001 From: Florentin Constancias Date: Thu, 14 Apr 2022 13:17:58 +0200 Subject: [PATCH] Update Microbiome_R_tutorial.Rmd addded microViz --- SOP/community_analyses/Microbiome_R_tutorial.Rmd | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/SOP/community_analyses/Microbiome_R_tutorial.Rmd b/SOP/community_analyses/Microbiome_R_tutorial.Rmd index 8556d45..aed114e 100644 --- a/SOP/community_analyses/Microbiome_R_tutorial.Rmd +++ b/SOP/community_analyses/Microbiome_R_tutorial.Rmd @@ -1912,6 +1912,18 @@ Select your data > RDS allows to directly load the phyloseq object. * [shiny-phyloseq](http://joey711.github.io/shiny-phyloseq/) +* [microViz](https://david-barnett.github.io/microViz/): microViz provides a Shiny app for an easy way to start exploring your microbiome data: all you need is a phyloseq object! + +```{r} +library(microViz) + +pseq <- readRDS("../../data-raw/ps_invivo.RDS") %>% + microViz::tax_fix() %>% + microViz::phyloseq_validate() + +ord_explore(pseq) +``` + ## qiime2: QIIME™ (pronounced chime) stands for Quantitative Insights Into Microbial Ecology. It is a bioinformatic pipeline developed to ease the process of bioinformatic analysis of raw sequencing microbiome data - not explored here since we have processed the data using [metabaRpipe](https://github.com/fconstancias/metabaRpipe). It is also useful to visualize and analyze the processed data, in a user friendly experience: