Problems with creating phyloseq bar plots from a table with species data
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lm795 ▴ 10
@lm795-17736
Last seen 2.9 years ago
United Kingdom

I am trying to plot species abundance for intestinal bacteria analysed using a 16S RNA sequencing method. I am using RStudio (1.1.456) and R 3.5.1 My input is a file called "Speciespercentagestest.csv", here. I was following the tutorial on "Importing phyloseq Data", more specifically, loading the table into phyloseq using the sample_data command. Here is my code:

BiocManager::install('phyloseq')
library(readr)
library(phyloseq)
library(ggplot2)
species_analysis <- read_csv("Species_percentages_test.csv")
theme_set(theme_bw())
species_p <- sample_data(species_analysis, errorIfNULL=TRUE)
taxa_are_rows(species_p)
plot_bar(species_p)

My issue is with the "taxaarerows" function. I believe I need to use it to specify the orientation of operational taxonomic units (OTUs), in my case "species" but I am none the wiser on how to apply this function in my specific example. I am sure this is a rookie question but this is the first time I deal with microbiome data. Your help is truly appreciated!

phyloseq microbiome analysis • 428 views
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