Adonis analysis

[ari_sh70]

Hello everyone,

I want to perform adonis analysis in R using the Bray-curtis matrix that I have. I do not know what the error is that I am getting.
I am using the following codes:

#Adonis analysis

library(tidyverse)
library(readxl)
library(vegan)

metadata <- read_excel("metadata.xlsx")

distance <- read_excel("bray_curtis.xlsx")
dist_mat <- distance %>% remove_rownames %>% column_to_rownames(var="sample_id")
colnames(dist_mat) <- c("sample_id")
meta_distance <- inner_join(metadata, distance, by="sample_id")

all_dist <- meta_distance %>%
  select(all_of(.[["sample_id"]])) %>%
  as.dist()

adonis(all_dist~Farm, data = meta_distance)

The bray_curtis matrix:

The metadata:

I would appreciate any help!

Thanks

[williaml]

Hi, can you provide reproducible examples of your dataset instead of screenshots?

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

[ari_sh70]

Yes, of course.

> head(metadata)
# A tibble: 6 x 14
  sample_id Farm  Variety Treat Location Treatment Copper BarcodeSequence
  <chr>     <chr> <chr>   <chr> <chr>    <chr>      <dbl> <chr>          
1 ID1468-1~ Moli~ PI      TE    West     soil        34.2 ACTCGCTATTATGC~
2 ID1468-1~ Moli~ PI      TE    West     soil        51.9 ACTCGCTAGAGCCT~
3 ID1468-1~ Moli~ PI      TE    West     soil        38.9 ACTCGCTAAAGGCT~
4 ID1468-1~ Moli~ PI      TE    West     soil        51.2 ACTCGCTACTATTA~
5 ID1468-1~ Moli~ PI      TE    West     soil        44.0 ACTCGCTAGCGTAA~
6 ID1468-1~ Moli~ PI      TE    East     soil        32.6 ACTCGCTACCTAGA~
# ... with 6 more variables: LinkerPrimerSequence <chr>, ReversePrimer <chr>,
#   LinkerPrimerSequence_RC <chr>, ReversePrimer_RC <chr>, Demultiplexer <chr>,
#   Description <chr>

> head(distance)
# A tibble: 6 x 49
  sample_id ID1468.16S.3 ID1468.16S.9 ID1468.16S.11 ID1468.16S.44 ID1468.16S.27
  <chr>            <dbl>        <dbl>         <dbl>         <dbl>         <dbl>
1 ID1468.1~        0            0.403         0.444         0.556         0.512
2 ID1468.1~        0.403        0             0.448         0.529         0.496
3 ID1468.1~        0.444        0.448         0             0.581         0.559
4 ID1468.1~        0.556        0.529         0.581         0             0.523
5 ID1468.1~        0.512        0.496         0.559         0.523         0    
6 ID1468.1~        0.635        0.600         0.671         0.560         0.598

Is it fine like this?

[nirgrahamuk]

Sorry, but no. Can you please read the guide ? its a relatively fast read and packed with useful information for interacting with the forum effectively. It really will benefit you in your search for help.