Sandeep Kumar

I find this temp. solution that might be useful to pool all the checkM result in one txt file from all samples. cd to bactopia output folder then, find ....

Dear @rpetit3, I am wondering abut use of Scoary (https://github.com/AdmiralenOla/Scoary) with bactopia and looking forward to see this as a bactopia tool. Thanks, Sandeep

Ok thanks, I'll give it a go on ROARY. Yes would be handy to have some visualization tools added, like Bandage etc. https://github.com/rrwick/Bandage Also, I can see you are already...

Many thanks.

Hi @ycl6, Could you please take this one step further and help me to plot stacked bar graph of top 5 genus (relative abundance)..? A very beginner's request. Thanks and...

Many Thanks @ycl6 , However I'm trying to reproduce this and getting the error below.. at sample name step > sn = sample_names(sample_data(rb)[sample_data(rb)$SampleType == type,]) Error in h(simpleError(msg, call)) :...

Thanks for quick reply @ycl6 . See the pic below for example.  So 5 genera would be in the legend and all other genera would ideally get grouped in...

Hi @ycl6, Yes looking great. just one last things. if we want to show two or more groups/sample types like Feces and Soil in one graph (like the one in...

Also When I am trying type = levels(sample_data(rb)$SampleType)[1] then the output is NULL which I think is because of, in GlobalPatterns Sample_data are stored as factor but in my own...

Thanks @ycl6 for detailed instructions now I feel I have all the information needed for visualisation.