Convert Distance matrix to Data Frame
meltDistanceToTable(x, dist_mat = NULL, name_dist_column = "value", ...)A phyloseq object
An object of class dist
A specific name for column where distance values are stored. Default="value"
Option to pass biomeUtils::getSampleTibble like column name and columns to be included in the output.
A data frame with pairwise distance and sample information
Converts dist object from phyloseq::distance()
to a data frame combined with sample data
library(biomeUtils)
data("FuentesIliGutData")
ps <- filterSampleData(FuentesIliGutData, ILI != "L2")
ps <- phyloseq::rarefy_even_depth(ps)
#> You set `rngseed` to FALSE. Make sure you've set & recorded
#> the random seed of your session for reproducibility.
#> See `?set.seed`
#> ...
dist.mat <- phyloseq::distance(ps, "bray")
dist.melt.sample <- meltDistanceToTable(ps,
dist_mat = dist.mat,
name_dist_column = "Bray-Curtis",
select_cols = c("participant_id", "ILI"))
head(dist.melt.sample)
#> S1 S2 Bray.Curtis participant_id_S1 ILI_S1 participant_id_S2
#> 1 sample_2 sample_1 0.5506150 ELD2 C ELD1
#> 2 sample_3 sample_1 0.5848747 ELD3 C ELD1
#> 3 sample_4 sample_1 0.5572665 ELD4 C ELD1
#> 4 sample_5 sample_1 0.6357175 ELD5 L1 ELD1
#> 5 sample_6 sample_1 0.7339408 ELD6 C ELD1
#> 6 sample_7 sample_1 0.5845103 ELD7 L1 ELD1
#> ILI_S2
#> 1 C
#> 2 C
#> 3 C
#> 4 C
#> 5 C
#> 6 C