ampvis2

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Add plot alpha diversity

2

We love that tool and currently plan to develop a series of use-case based tutorials using Galaxy. See https://github.com/usegalaxy-eu/project-ideas/issues/41 We will probably also work on using the shiny app as...

paulzierep

Thank you for using ampvis2! If you encounter a problem with ampvis2 that you are unable to resolve, this is the place for discussing the problem with developers to find...

KasperSkytte

Heatmap normalise_by only works by sample names

4

According to the docs I can > A variable or a specific sample in the metadata to normalise the counts by. If I do ``` amp_heatmap(AalborgWWTPs, normalise=T, normalise_by = 'Plant')...

bernt-matthias

How to `group_by` in `use amp_frequency`

2

I'm trying ``` data("AalborgWWTPs") amp_frequency(AalborgWWTPs, group_by = "Plant") ``` but I get: ``` Error in apply(data$metadata[, group_by], 1, paste, collapse = " ") : dim(X) must have a positive length...

bernt-matthias

I often have count tables that have an empty string in the header that marks the OTU/ASV column. So far I could not find a way to handle this directly...

bernt-matthias

I have troubles plotting functions in `amp_heatmap` when setting `tax_aggregate = 'Species'` as shown in example below: ``` amp_heatmap(data, group_by = 'SampleSite', normalise = F, tax_aggregate = 'Species', tax_add =...

SofieZacho

Just wanted to ask if you can tell me what kind of metadata variables are supposed as input to the tools. I hope that a PR is a nice way...

bernt-matthias