cpauvert/psadd

PSADD -- PhyloSeq ADDitions

psadd's Issues

No longer supported?

Is this package no longer supported in R? When I try to run it it tells me KronaTools are not installed.

Error in plot_krona function

Hello @cpauvert

Thank you for developing this package. I use this to create a krona plot from the mothur share file, which runs smoothly. However, when I use qiime2 files as an input for phyloseq object, I get this error:

Error in `[.data.frame`(df, , c("Abundance", variable, rank_names(physeq))) : undefined columns selected Calls: plot_krona -> [ -> [.data.frame

This is my command: plot_krona(physeq_do, "GP-krona", "sample_id", trim = F)

Is something that I miss here?

Thank you

plot_krona() unable to work without KronaTools

Hi Charlie,

I'm looking to use the plot_krona() function in R studio for some microbiome analyses.

I had installed the dependencies for krona using your code:
remotes::install_github("cpauvert/psadd")

Upon running plot_krona(), the following error would appear:
KronaTools are not installed. Please see https://github.com/marbl/Krona/wiki/KronaTools.

I have learned that KronaTools is a command line package, so I downloaded in Ubuntu using the code:

Install KronaTools

curl -LOk https://github.com/marbl/Krona/releases/download/v2.8.1/KronaTools-2.8.1.tar

tar xvf KronaTools-2.8.1.tar

cd KronaTools-2.8.1

sudo ./install.pl

However, I get the same error when running plot_krona() in R studio.

IS there something I'm missing? Any advice greatly appreciated.

Best,
Angelica