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Fill a Bar Plot with Taxonomic Grouping #1398

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stevenbressan opened this issue Oct 9, 2020 · 0 comments
Open

Fill a Bar Plot with Taxonomic Grouping #1398

stevenbressan opened this issue Oct 9, 2020 · 0 comments

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@stevenbressan
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Hello, I would like to make a bar plot to see relative abundance of each genus present in my samples. However, following the basic tutorial, using the command plot_bar(euk_phyt, x="Genus") does not work, as "Genus" it not recognized as a variable.

For the following commands: euk_phyt returns phyloseq-class experiment-level object otu_table() OTU Table: [ 441 taxa and 6 samples ] sample_data() Sample Data: [ 6 samples by 10 sample variables ] tax_table() Taxonomy Table: [ 441 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 441 tips and 440 internal nodes ]
While the command sample_variables(euk_phyt) returns [1] "Area" "Stratum" "Adj_MSRR" "resp_bin" "ln_LOI_550" "loi_bin" [7] "density_bin" "SDBD" "Year.CE" "Comments"

My question is, how can I used the plot_bar command and tell phyloseq to fill based off of the genus grouping in my taxonomy table? Currently fill only seems to be available from the variables listed by the sample_variable command.

Thank you for the help.

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