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Albert Vill authored Aug 27, 2021
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## Using the app

Upload your merged Bracken file and click "Create Plot". The app will automatically detect the taxonomic level and print a stacked bar plot showing relative abundance of each taxa. Often, there are many taxa with near-zero abundances, and plotting all taxa results in ambiguous labeling. If this is the case, use the "Maximum number of taxa to plot" field to subsample the dataset. Subsampling will reduce the number of taxa plotted to the *n* taxa with the greatest median relative abundances across samples. The relative abundances of all taxa not in the subset are summed and plotted as "other".
Upload your merged Bracken file and click "Create Plot". To plot an example, you can download Bracken output files from [this repository](https://github.com/acvill/bracken_plot/tree/main/example_data_bracken). The app will automatically detect the taxonomic level and print a stacked bar plot showing relative abundance of each taxa. Often, there are many taxa with near-zero abundances, and plotting all taxa results in ambiguous labeling. If this is the case, use the "Maximum number of taxa to plot" field to subsample the dataset. Subsampling will reduce the number of taxa plotted to the *n* taxa with the greatest median relative abundances across samples. The relative abundances of all taxa not in the subset are summed and plotted as "other".

Custom color palettes can be added as a string of comma-separated hexadecimal values without spaces or `#` characters. Colors are recycled in cases where the number of taxa exceeds the number of colors in a palette. If subsampling taxa, make sure that custom palettes do not contain the color used for the "other" label (gray `808080` by default). Some example palettes:

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