Amazing video. Thank you for sharing. Please make more of these videos on microbiome analyses. e.g beta diversity, pcoa, NMDS, community heat map, serial group comparisons etc
amazing, thank you! combining all the metabarcoding data in one large table and visualizing with ggplot is much more handy to work with than phyloseq. best regards :)
Thank you for your video, and I really enjoy and successfully plotted the graph through the tutorial. Anyway, if I apply it to the real work, I would like to know how you calculated the aboundancy %?
Hi Thank you for your video, please i would like to know the metagenomic analysis tool that you used and why your OTU ID are coded because mine are long numeric number and i used QIIME2
There is more than one way to do it. You can see how I did it in the extended_example.Rmd file of the GitHub repo. Or go to this link github.com/surh/scip_barplot/blob/a775e0d97b47e8dd40498b6713016bbb7e045003/extended_example.Rmd#L285-L301
I'm general it is not a good idea to represent that many levels with color, the human eye and brain just can't distinguish that many times. Ten is already pushing it and that is my common limit. You should think how to group those 50 levels in a meaningful way. If you really need to show 50 different groups (which generally you don't) then this type of barplot is not the right plot.
Thank you very much for the explanations! The comands of Tidyverse are amazing and so useful!!!!!!!!
Amazing video. Thank you for sharing. Please make more of these videos on microbiome analyses. e.g beta diversity, pcoa, NMDS, community heat map, serial group comparisons etc
Thank for the vdo. Please keep this type of tutorial vdo coming.
Thank you for your teaching and sharing. It helps me a lot. Really appreciate.
amazing, thank you! combining all the metabarcoding data in one large table and visualizing with ggplot is much more handy to work with than phyloseq. best regards :)
Gracias por este video hermanoo!! no tiene abuela este cientifico!!!
Thank you for your video. Could you tell the how to get the mean abundence percentage table?
remarkable lecture
Dear Dr, please share us if you have video lecture related to indicator species analysis in r
Thank you so much for this video!! so clear
Thank you for your video, and I really enjoy and successfully plotted the graph through the tutorial.
Anyway, if I apply it to the real work, I would like to know how you calculated the aboundancy %?
It's amazing. How can I find prompt to make mean abundance?
How to calculate the mean abundance, sir ? I hope you can provide an answer. Thank you so much :)
How to know the code or command line to achieve such table with otu ?
Can you tell me which package can be used for prevalence calculation for Microbiome Data.
Hi Thank you for your video, please i would like to know the metagenomic analysis tool that you used and why your OTU ID are coded because mine are long numeric number and i used QIIME2
the OTUs and samples are subset of the data from this paper (www.nature.com/articles/nature11237), we built the OTUs with usearch
Thank you for the video. I just would love to know who you imported the data, and if it should be tsv format? Thanks
All the data and code is the github repo github.com/surh/scip_barplot
The data is in tsv format so I used the read_tsv function of the readr package
How were you able to obtain the mean abundance to be able to reorder the Phylum?
There is more than one way to do it. You can see how I did it in the extended_example.Rmd file of the GitHub repo. Or go to this link github.com/surh/scip_barplot/blob/a775e0d97b47e8dd40498b6713016bbb7e045003/extended_example.Rmd#L285-L301
I have been struggling to this, honestly
How to plot the relative abundance of the most abundant genera (with a mean relative abundance > 1% in all samples? please
How can I get the diversity based on this?
Hi what if i have 50 legends? Cannot do it with rcolorbrewer and rainbow color is not that presentable.
I'm general it is not a good idea to represent that many levels with color, the human eye and brain just can't distinguish that many times. Ten is already pushing it and that is my common limit. You should think how to group those 50 levels in a meaningful way. If you really need to show 50 different groups (which generally you don't) then this type of barplot is not the right plot.
Gracias
😃thank you