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Commit 1250426c authored by Simeon's avatar Simeon
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all analyses re-knitted

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--- ---
title: "16S Data Analysis" title: "OITS Data Analysis"
author: "Simeon Lim Rossmann, Marte Persdatter Tangvik" author: "Simeon Lim Rossmann, Marte Persdatter Tangvik"
date: "23.12.2024" date: "23.12.2024"
output: output:
...@@ -86,7 +86,7 @@ remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev") ...@@ -86,7 +86,7 @@ remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev")
source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R" ) source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R" )
library(phyloseq) library(phyloseq)
library(SIAMCAT) #library(SIAMCAT)
# Phylogeny libraries # Phylogeny libraries
library(phangorn) library(phangorn)
...@@ -668,7 +668,7 @@ oomycetes_percentage ...@@ -668,7 +668,7 @@ oomycetes_percentage
This chunk plots abundance of the Top n ASVs or taxa at a given level as a bar plot, giving an insight into the presence of the n ASV and most common taxa for the primary and secondary parameters. The default for n is set at 20, a larger n may lead to delay/skipping of the plot in standard out, but it should be saved as a PDF regardless for ASVs. For taxa, a large n may lead to unreadable plots. **The chunk does not require any input**, but it is possible to adjust the **default 'n'**, and to change **width**, **height** and **resolution** of the PDF-output if necessary. This chunk plots abundance of the Top n ASVs or taxa at a given level as a bar plot, giving an insight into the presence of the n ASV and most common taxa for the primary and secondary parameters. The default for n is set at 20, a larger n may lead to delay/skipping of the plot in standard out, but it should be saved as a PDF regardless for ASVs. For taxa, a large n may lead to unreadable plots. **The chunk does not require any input**, but it is possible to adjust the **default 'n'**, and to change **width**, **height** and **resolution** of the PDF-output if necessary.
```{r custom-Bar-plot, tidy=TRUE, message=FALSE} ```{r custom-Bar-plot, message=FALSE}
# CHANGE ME to the desired sample categories on the x-axis. # CHANGE ME to the desired sample categories on the x-axis.
...@@ -784,7 +784,7 @@ topntax_data <- set$topntax_tbl %>% ...@@ -784,7 +784,7 @@ topntax_data <- set$topntax_tbl %>%
select(Alias, ndvi, Shannon, Taxa) %>% select(Alias, ndvi, Shannon, Taxa) %>%
distinct() distinct()
write.csv(topntax_data, file = "../../topntax_all_taxa/topntax_data_oomycetes.csv") write.csv(topntax_data, file = "../topntax_all_taxa/topntax_data_oomycetes.csv")
``` ```
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