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:
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 “130×131” how can I prevent this? I cannot run metaMDS without having this formatted as a distance-matrix.
Thank you in advance!
Read more here: Source link