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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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error: data length [] is not a sub-multiple or multiple of the number of rows [] #1643

Closed marwa38 closed 1 year ago

marwa38 commented 1 year ago

Hi .. I have the same issue as #643 and #1574 but you were not able to help I think because of the lack of reproducible example? so here I share a reproducible example to help find out the reason behind this error Cheers

library(phyloseq)
phyloseq::distance(ps.prev.intes.tree.rare, method="unifrac", weighted=F)

image

attached the input data (phyloseq object) zipped .rds ps.prev.intes.tree.rare.zip @ycl6

ycl6 commented 1 year ago

Hi @marwa38 The discussion in https://github.com/joey711/phyloseq/issues/936 will be of interest to you.

In short, the distance calculation only works when your tree is a binary tree. Hence after pruning, you might need to re-construct the phylogenetic tree to obtain a binary tree, or in the example below uses multi2di() to transforms multichotomies into a series of dichotomies.

library(phyloseq)
library(ape) # is.binary, multi2di

ps = readRDS(file = "ps.prev.intes.tree.rare.rds")
ps
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1314 taxa and 79 samples ]
#> sample_data() Sample Data:       [ 79 samples by 10 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1314 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 1314 tips and 1302 internal nodes ]

ps_tree = phy_tree(ps)
ps_tree
#> 
#> Phylogenetic tree with 1314 tips and 1302 internal nodes.
#> 
#> Tip labels:
#>   ASV4394, ASV1361, ASV5153, ASV1082, ASV4334, ASV5021, ...
#> Node labels:
#>   Root, 0.000, 0.966, 0.862, 0.917, 0.911, ...
#> 
#> Rooted; includes branch lengths.

# Check if binary (dichotomy) & multifurcating (polytomy) trees
sprintf("Is tree binary: %s", is.binary(ps_tree))
#> [1] "Is tree binary: FALSE"

# If FASLE, randomly resolve polytomies and replace tree in "ps"
phy_tree(ps) = multi2di(ps_tree)
sprintf("Is tree binary: %s", is.binary(phy_tree(ps)))
#> [1] "Is tree binary: TRUE"

dist = phyloseq::distance(ps, method = "unifrac", weighted = F)
sprintf("`dist` class: %s", class(dist))
#> [1] "`dist` class: dist"

Created on 2022-11-29 by the reprex package (v2.0.1)

marwa38 commented 1 year ago

thank you so much