qiime2 distance matrix as input for R

General Discussion
1

Hello,

I'm trying to analyse skin Microbiota from human samples. (V3-V4 Illumina Miseq.) I finished the moving pictures tutorial up to the point of creating the distance matrices, everything looks neat.

Now I'd like to take these results into R to create PCoA Plots.

1.) I exported the Bray-Curtis-Distance-Matrix from qiime2 via this command:

qiime tools export --input-path bray_curtis_distance_matrix.qza --output-path bray-curtis-for-R

This gives me a .tsv file which looks like this:

image
image970×404 79.8 KB

So far, so good.

2.) Now I'd like to feed this table as a distance matrix into R.

library("readr")
dist_bray <- read_tsv('distance-matrix-for-R.tsv')
print(dist_bray)

> print(dist_bray)
# A tibble: 130 × 131
   ...1      1-12-…¹ 1-12-…² 1-12-…³ 1-8-3…⁴ 1-8-3…⁵ 1-8-3…⁶ 2-21-…⁷ 2-21-…⁸ 2-21-…⁹ 3-15-…˟ 3-15-…˟
   <chr>       <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>

Whenever I try to feed this into as.dist-Function (be it as a df or a tibble) I get the following error message:

> imported_dist_matrix<-as.dist(dist_bray_df)
Warning messages:
1: In storage.mode(m) <- "numeric" : NAs introduced by coercion
2: In as.dist.default(dist_bray_df) : non-square matrix
> imported_dist_matrix<-as.dist(dist_bray)
Warning messages:
1: In storage.mode(m) <- "numeric" : NAs introduced by coercion
2: In as.dist.default(dist_bray) : non-square matrix

Why does my qiime2-Distance matrix turn non-square as indicated by the "130x131" how can I prevent this? I cannot run metaMDS without having this formatted as a distance-matrix.

Thank you in advance!

1 Like
2

I solved my issue like this. In the end it all boiled down to basic R things like what is a tibble vs a matrix vs a dataframe.
The solution was: set column names to TRUE and omit the row names

dist_bray <- read_tsv(file='distance-matrix-for-R.tsv', col_names=TRUE)
dist_bray[1] <- NULL
correct<-as.dist(dist_bray)
metaMDS(correct)

I'm just leaving this here in case anyone else will find this useful in the future.

Best Regards!

1 Like