microViz

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tax.fix(), and "Problematic Genus values detected in tax_table"

2

Hello! I am having an issue with the tax.fix() command. Using the command like this: phyloseq object %>% tax_fix( min_length = 4, unknowns = c("."), #Unknowns in taxon table are...

Nekovirus

Error in access(object, "otu_table", errorIfNULL) : otu_table slot is empty.

2

Hi, I have a problem plotting relative abundance for some of my samples. This is my phyloseq object, which definitely has an OTU table: ``` > p2 phyloseq-class experiment-level object...

chrstraub

cor_heatmap taxon_renamer or alternative option for labeling rows

2

Hi David! I am trying my luck at generating some correlation plots, following your tutorials [here](https://david-barnett.github.io/microViz/articles/web-only/heatmaps.html#correlation-heatmaps). I would like to change the row labels to specify ASV number and Species...

AngelicaMiraples

comp_barplot seem to have issues with domain being unknown

1

Hello, I have an ASV where all levels are unknown as following: `Taxonomy Table: [1 taxa by 7 taxonomic ranks]: Domain Phylum Class Order Family Genus Species 55b5947908a70f952516e813b1ca9e71 "Unclassified" "Unclassified"...

NeginValizadegan

Taxa cannot be aggregated at rank: Genus

1

I have been facing significant challenges with the "Taxa cannot be aggregated at rank: Genus tax_agg" issue, especially when inconsistencies at the previous taxonomic level are unavoidable, particularly during denovo...

bylam

phylogenetic tree disappeared after tax_transform() step

1

Hi, I'm trying to plot ordination plot, so I used the below code: ``` ps0 %>% tax_fix() %>% phyloseq_validate() %>% tax_transform("clr", rank = "Genus") %>% dist_calc(dist = "wunifrac") %>% ord_calc(constraints...

Leran10

Cannot build PCoA plot using ord_plot

1

Dear Davit, Thank you for your very useful and cute package, Microviz. With my student we are having problems building PCoA plot with ord_plot function. We get the following error...

LauGuaUuu

dominant taxa in each sample

2

I have two issues. 1) on the figure attached. some samples clearly have a dominant genera but it is labelled 'other' on the bar. e.g the last sample on the...

momodiame21

p values in correlation heatmaps

5

Hello David, I want to ask another question; how can I show the p-values of the spearman correlation in the correlation heatmap?

BrigittevdG

The `tax_filter` argument `min_sample_abundance` does not recognise proportions

2

Hello, and thank you for an excellent R package! I have a dataset and I want to prune taxa that has a relative abundance of less than 0.1% on the...

hkaspersen