Color palette, rgb, color name etc... or possible insertion from other packages? about fantaxtic HOT 9 CLOSED

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@gmteunisse thank you for the fast reply!

I saw the palette section, I was wondering if instead of using:

 palette = c(Bacteroidetes = "red", 
                            Proteobacteria = "blue"),

I can also use a personalized object like this or directly a command of RColorBrewer

colourCount1=length(get_taxa_unique(e1_sub, taxonomic.rank = "Genus"))

pal <- colorRampPalette(brewer.pal(12,"Paired"))(colourCount1))

plot_nested_bar(top_e1$ps_obj,
                top_level = "Class",
                nested_level = "Genus",
                nested_merged_label = "NA and other <tax>",
                palette= pal,
                legend_title = "Phyla and genera") 

to assign the colour to the nested_level? e.g. trying this, just a blue color appears in the plot.

If that is not possible, could I also provide a color code in hex, like this, when defining the palette with taxoun_colours()?

pal3 <- taxon_colours(top_e1$ps_obj, 
                     tax_level = "Phylum", 
                     palette = c(Alphaproteobacteria = "#6d4c3d", 
                                 Campylobacterota = "#095256",
                                Gammaproteobacteria= "#ec7357"))

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Yes, is working but is following the order of priority (I suppose) that RColorBrewer give in the adopted palette...moreover, I have a sample with really low diversity in terms of top_level. I'm plotting with class and genus. So, probably this makes the barplot not completely differentiated aesthetically as I had in mind.

Probably, a suitable alternative for me, could be to better define the plot with the advance usage settings. Can I group the genus less abundant then 5% and NA, make the nested legends and plot it using ggplot, right?

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Indeed, this is what I mean with my second question: they are samples from enrichment (most of them), which makes the top level not diverse also at class level, which is my actual top level.

I can manage the colour to arrange it down to the order or family. I want to know if there is a way to have a significant control on the filtering level when choosing the top_taxa.

I'm working on that:

top_e1 <- top_taxa(e1_sub,
                        n_taxa = 10,
                        tax_level = "Genus",
                        grouping = "Sample_id")

If I want to drop all the taxa below a specific value (e.g. less than 10% abundant) and group these together using a label Less abundant < 10% or similar... is there a way to do that in fantaxtic? So, with more fine-tuned filtering.

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There’s no native support for that, but you can use some fantaxtic helper functions to do so. You would need to identify the taxon ids of the taxa that you want to merge; fantaxtic can do the rest. See this issue for a code example for merging:
#25

See this stackoverflow answer for an approach of identifying taxa by %: https://stackoverflow.com/questions/76631141/filter-phyloseq-to-use-in-fantaxtic

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Thank you for the reply and sorry for mine late one.

The second example is working perfectly; I have two additional questions to end that:

In your opinion, what is the difference between using max and sum? It probably is not really clear to me what max is doing.

The second question...plot_nested_bar is a ggplot object, so it can be treated equally. Can I modify the aesthetic parameters of the plot without modifying/losing the legend organization? on the way around, there is a way to reproduce the same legend organization in fantaxtic in a normal ggplot taxa plotbar?

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