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Questions - phyloseq

phyloseq: Discrepancies in otu counts before and after using tax_glom

Maybe I missed something in how tax_glom works but as I did not find any info here nor elsewhere on the web, maybe someone here can help. I do not provide data but I can on request. Here is the code h...
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GTC

r

phyloseq

Votes: 0

Answers: 1

Latest Answer

The NArm term in the tax_glom function is, by default, set as TRUE. To avoid losing observations with NA cells you need to set the NArm = FALSE. Cheers
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Zina

After separating into columns, how do I sort my data so that it's in the right column?

I have a taxonomy list created from bracken that I want to import to phyloseq. I have my taxa in one column like so: k__Bacteria|p__Coprothermobacterota|c__Coprothermobacteria|o__Coprothermobacterales...
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sisherb

r

taxonomy

phyloseq

Votes: 0

Answers: 1

Latest Answer

You can do use strsplit, and then pivot_wider() like this: d %>% mutate(taxs = strsplit(taxonomy,split="|",fixed=TRUE), rowid =row_number()) %>% unnest(taxs) %>% s...
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langtang

Fail to plot by group on a phyloseq object generated by R package Divnet

I intend to plot an alpha diversity plot of my samples, which consist of three groups. Alpha diversity is calculated by R package Divnet. It involve using phyloseq as a dependency. The group of each s...
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ivanllam

r

ggplot2

phyloseq

Votes: 0

Answers: 1

Latest Answer

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally,...
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danlooo

phyloCorrelogram() issues

I've been struggling with phyCorrelogram() from the package phylobase. I have received a myriad of errors this past month, and I have come full circle with the first error again. (yay) I am enormously...
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Geomicro

r

phylogeny

phyloseq

Votes: 0

Answers: 0

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